All I have to do is delete any resource and the rebuild resources and the deleted resource pops back up but points to the next highest resource number. For example, I've just tried this with palettes. I have two palettes. 998 and 999. 998 is the SQ5 palette and 999 is the KQ5 palette. I kept the SQ5 one just in case. I decided that I didn't need it anymore and deleted it. After rebuilding resources 998 popped back but its number is set to 999 (as opposed to its name) and when opening either palette it opens palette 999 for editing. If I delete 998 again and rebuild resources nothing exists because I deleted 999 so it deleted both entries.
This brings up another bug that I've also run into before. When I try to create a new palette and attempt to save it to the game I can set any number I want, but the package number is set to 63 and can't be changed (it's greyed out). Attempting to save to a resource number fails because it complains that it can't find resource package 64. I have to actually edit an existing palette (or any resource) and then save as a new number to create new resources from scratch. Creating new blank resources doesn't allow saving.
Here's a resource map dump from a brand new game just after I've added and deleted a 998.pal resource and then rebuilt resources (which brings 998 back in name, but its number is set to 999 in the list):
Resource map for New Game
Type: 80 Offset: 002b
Type: 81 Offset: 0080
Type: 82 Offset: 0099
Type: 83 Offset: 0265
Type: 84 Offset: 0283
Type: 86 Offset: 0292
Type: 87 Offset: 02a6
Type: 89 Offset: 02bf
Type: 8b Offset: 02d3
Type: 8f Offset: 02dd
Type: 90 Offset: 0305
Type: 91 Offset: 030a
Type: ff Offset: 04e0
0027: 00 00 00 00 00 View(0, 0) offset: 00000000
0027: 0D 00 25 1E 00 View(13, 0) offset: 00003C4A
0027: 84 03 1D 3D 00 View(900, 0) offset: 00007A3A
0027: D4 03 8C 3E 00 View(980, 0) offset: 00007D18
0027: D5 03 93 42 00 View(981, 0) offset: 00008526
0027: D6 03 DA 42 00 View(982, 0) offset: 000085B4
0027: D7 03 24 43 00 View(983, 0) offset: 00008648
0027: D8 03 F0 43 00 View(984, 0) offset: 000087E0
0027: DD 03 C0 44 00 View(989, 0) offset: 00008980
0027: DE 03 14 45 00 View(990, 0) offset: 00008A28
0027: DF 03 9F 4B 00 View(991, 0) offset: 0000973E
0027: E3 03 B3 4F 00 View(995, 0) offset: 00009F66
0027: E4 03 3B 65 00 View(996, 0) offset: 0000CA76
0027: E5 03 7D 65 00 View(997, 0) offset: 0000CAFA
0027: E7 03 0B 66 00 View(999, 0) offset: 0000CC16
0027: D0 07 59 66 00 View(2000, 0) offset: 0000CCB2
0027: 33 08 A0 6E 00 View(2099, 0) offset: 0000DD40
0027: 00 00 A0 74 00 Pic(0, 0) offset: 0000E940
0027: 1F 00 D2 74 00 Pic(31, 0) offset: 0000E9A4
0027: 6E 00 50 EB 00 Pic(110, 0) offset: 0001D6A0
0027: C8 00 F5 64 01 Pic(200, 0) offset: 0002C9EA
0027: 2C 01 9F 6B 01 Pic(300, 0) offset: 0002D73E
0027: 00 00 D2 8C 01 Script(0, 0) offset: 000319A4
0027: 0B 00 67 97 01 Script(11, 0) offset: 00032ECE
0027: 0C 00 BB 97 01 Script(12, 0) offset: 00032F76
0027: 0D 00 0E 98 01 Script(13, 0) offset: 0003301C
0027: 0E 00 26 98 01 Script(14, 0) offset: 0003304C
0027: 0F 00 9C 98 01 Script(15, 0) offset: 00033138
0027: 10 00 21 9A 01 Script(16, 0) offset: 00033442
0027: 11 00 44 9B 01 Script(17, 0) offset: 00033688
0027: 12 00 B9 9D 01 Script(18, 0) offset: 00033B72
0027: 13 00 A7 9F 01 Script(19, 0) offset: 00033F4E
0027: 14 00 78 A1 01 Script(20, 0) offset: 000342F0
0027: 15 00 6F A2 01 Script(21, 0) offset: 000344DE
0027: 16 00 B7 A2 01 Script(22, 0) offset: 0003456E
0027: 18 00 B3 A4 01 Script(24, 0) offset: 00034966
0027: 19 00 AF A7 01 Script(25, 0) offset: 00034F5E
0027: 1A 00 75 A9 01 Script(26, 0) offset: 000352EA
0027: 1B 00 09 AD 01 Script(27, 0) offset: 00035A12
0027: 1E 00 3E AE 01 Script(30, 0) offset: 00035C7C
0027: 20 00 42 B3 01 Script(32, 0) offset: 00036684
0027: 64 00 1D B4 01 Script(100, 0) offset: 0003683A
0027: 69 00 76 B5 01 Script(105, 0) offset: 00036AEC
0027: 6E 00 AF B5 01 Script(110, 0) offset: 00036B5E
0027: CD 00 04 B6 01 Script(205, 0) offset: 00036C08
0027: FF 00 D0 B6 01 Script(255, 0) offset: 00036DA0
0027: 6D 03 86 BC 01 Script(877, 0) offset: 0003790C
0027: 99 03 AB BE 01 Script(921, 0) offset: 00037D56
0027: 9A 03 B4 C3 01 Script(922, 0) offset: 00038768
0027: 9B 03 0B C6 01 Script(923, 0) offset: 00038C16
0027: 9C 03 9D C8 01 Script(924, 0) offset: 0003913A
0027: 9D 03 73 CA 01 Script(925, 0) offset: 000394E6
0027: 9E 03 86 CC 01 Script(926, 0) offset: 0003990C
0027: 9F 03 69 CD 01 Script(927, 0) offset: 00039AD2
0027: A0 03 D0 CF 01 Script(928, 0) offset: 00039FA0
0027: A1 03 43 D6 01 Script(929, 0) offset: 0003AC86
0027: A2 03 AF D7 01 Script(930, 0) offset: 0003AF5E
0027: A4 03 7B D8 01 Script(932, 0) offset: 0003B0F6
0027: A5 03 3B D9 01 Script(933, 0) offset: 0003B276
0027: A6 03 05 DA 01 Script(934, 0) offset: 0003B40A
0027: A7 03 D2 DB 01 Script(935, 0) offset: 0003B7A4
0027: A8 03 3F DC 01 Script(936, 0) offset: 0003B87E
0027: A9 03 DB DD 01 Script(937, 0) offset: 0003BBB6
0027: AA 03 83 E6 01 Script(938, 0) offset: 0003CD06
0027: AB 03 FE E6 01 Script(939, 0) offset: 0003CDFC
0027: AD 03 5C E7 01 Script(941, 0) offset: 0003CEB8
0027: AE 03 08 E8 01 Script(942, 0) offset: 0003D010
0027: AF 03 BA E8 01 Script(943, 0) offset: 0003D174
0027: B0 03 C4 F5 01 Script(944, 0) offset: 0003EB88
0027: B1 03 AB F6 01 Script(945, 0) offset: 0003ED56
0027: B2 03 A5 F7 01 Script(946, 0) offset: 0003EF4A
0027: B3 03 E3 F7 01 Script(947, 0) offset: 0003EFC6
0027: B4 03 CA 0A 02 Script(948, 0) offset: 00041594
0027: B5 03 5E 11 02 Script(949, 0) offset: 000422BC
0027: B6 03 BE 11 02 Script(950, 0) offset: 0004237C
0027: B7 03 5D 14 02 Script(951, 0) offset: 000428BA
0027: B9 03 B0 14 02 Script(953, 0) offset: 00042960
0027: BA 03 2A 15 02 Script(954, 0) offset: 00042A54
0027: BB 03 90 17 02 Script(955, 0) offset: 00042F20
0027: BC 03 0F 18 02 Script(956, 0) offset: 0004301E
0027: BE 03 49 18 02 Script(958, 0) offset: 00043092
0027: C1 03 71 18 02 Script(961, 0) offset: 000430E2
0027: C3 03 28 19 02 Script(963, 0) offset: 00043250
0027: C4 03 67 19 02 Script(964, 0) offset: 000432CE
0027: C7 03 FF 19 02 Script(967, 0) offset: 000433FE
0027: C8 03 4F 1A 02 Script(968, 0) offset: 0004349E
0027: C9 03 03 1C 02 Script(969, 0) offset: 00043806
0027: CA 03 3A 1C 02 Script(970, 0) offset: 00043874
0027: CB 03 A3 1C 02 Script(971, 0) offset: 00043946
0027: CC 03 63 1D 02 Script(972, 0) offset: 00043AC6
0027: CD 03 ED 1D 02 Script(973, 0) offset: 00043BDA
0027: CF 03 3B 1F 02 Script(975, 0) offset: 00043E76
0027: D0 03 EC 1F 02 Script(976, 0) offset: 00043FD8
0027: D1 03 9B 21 02 Script(977, 0) offset: 00044336
0027: D2 03 75 23 02 Script(978, 0) offset: 000446EA
0027: D4 03 7B 25 02 Script(980, 0) offset: 00044AF6
0027: D5 03 C7 25 02 Script(981, 0) offset: 00044B8E
0027: D6 03 E1 26 02 Script(982, 0) offset: 00044DC2
0027: D7 03 7F 27 02 Script(983, 0) offset: 00044EFE
0027: D8 03 48 28 02 Script(984, 0) offset: 00045090
0027: D9 03 DB 29 02 Script(985, 0) offset: 000453B6
0027: DA 03 8D 2A 02 Script(986, 0) offset: 0004551A
0027: DB 03 30 2B 02 Script(987, 0) offset: 00045660
0027: DC 03 E7 2C 02 Script(988, 0) offset: 000459CE
0027: DD 03 5F 2E 02 Script(989, 0) offset: 00045CBE
0027: DE 03 E0 2F 02 Script(990, 0) offset: 00045FC0
0027: DF 03 95 35 02 Script(991, 0) offset: 00046B2A
0027: E0 03 59 37 02 Script(992, 0) offset: 00046EB2
0027: E1 03 C9 39 02 Script(993, 0) offset: 00047392
0027: E2 03 A3 3A 02 Script(994, 0) offset: 00047546
0027: E3 03 F6 42 02 Script(995, 0) offset: 000485EC
0027: E4 03 34 4A 02 Script(996, 0) offset: 00049468
0027: E6 03 46 4C 02 Script(998, 0) offset: 0004988C
0027: E7 03 95 53 02 Script(999, 0) offset: 0004A72A
0027: 0A 00 60 58 02 Text(10, 0) offset: 0004B0C0
0027: C9 00 BE 58 02 Text(201, 0) offset: 0004B17C
0027: CC 01 C7 58 02 Text(460, 0) offset: 0004B18E
0027: AF 03 D0 58 02 Text(943, 0) offset: 0004B1A0
0027: B8 03 1C 59 02 Text(952, 0) offset: 0004B238
0027: E7 03 52 59 02 Text(999, 0) offset: 0004B2A4
0027: 2D 00 6E 59 02 Sound(45, 0) offset: 0004B2DC
0027: E8 03 E2 5B 02 Sound(1000, 0) offset: 0004B7C4
0027: E9 03 14 5C 02 Sound(1001, 0) offset: 0004B828
0027: E2 03 7C 61 02 Vocab(994, 0) offset: 0004C2F8
0027: E4 03 B8 61 02 Vocab(996, 0) offset: 0004C370
0027: E5 03 DF 62 02 Vocab(997, 0) offset: 0004C5BE
0027: E6 03 DB 80 02 Vocab(998, 0) offset: 000501B6
0027: 00 00 55 82 02 Font(0, 0) offset: 000504AA
0027: 04 00 C4 85 02 Font(4, 0) offset: 00050B88
0027: E7 03 4D 88 02 Font(999, 0) offset: 0005109A
0027: 45 06 B3 8A 02 Font(1605, 0) offset: 00051566
0027: 3A 08 92 8D 02 Font(2106, 0) offset: 00051B24
0027: 01 00 01 91 02 Patch(1, 0) offset: 00052202
0027: 03 00 38 B7 02 Patch(3, 0) offset: 00056E70
0027: 04 00 C0 C1 02 Patch(4, 0) offset: 00058380
0027: 65 00 54 C4 02 Patch(101, 0) offset: 000588A8
0027: E6 03 6E C5 02 Palette(998, 0) offset: 00058ADC
0027: E7 03 03 C6 02 Palette(999, 0) offset: 00058C06
0027: 00 00 98 C6 02 Message(0, 0) offset: 00058D30
0027: 0D 00 31 CD 02 Message(13, 0) offset: 00059A62
0027: 0F 00 63 CD 02 Message(15, 0) offset: 00059AC6
0027: 14 00 89 CE 02 Message(20, 0) offset: 00059D12
0027: 69 00 A1 CE 02 Message(105, 0) offset: 00059D42
0027: 6E 00 BF CE 02 Message(110, 0) offset: 00059D7E
0027: DE 03 10 CF 02 Message(990, 0) offset: 00059E20
0027: E2 03 8E D0 02 Message(994, 0) offset: 0005A11C
0027: FF FF 57 D1 02 Map(65535, 0) offset: 0005A2AE
0027: 00 00 61 D1 02 Heap(0, 0) offset: 0005A2C2
0027: 0B 00 31 D5 02 Heap(11, 0) offset: 0005AA62
0027: 0C 00 4A D5 02 Heap(12, 0) offset: 0005AA94
0027: 0D 00 53 D5 02 Heap(13, 0) offset: 0005AAA6
0027: 0E 00 6B D5 02 Heap(14, 0) offset: 0005AAD6
0027: 0F 00 93 D5 02 Heap(15, 0) offset: 0005AB26
0027: 10 00 4B D7 02 Heap(16, 0) offset: 0005AE96
0027: 11 00 79 D7 02 Heap(17, 0) offset: 0005AEF2
0027: 12 00 AF D7 02 Heap(18, 0) offset: 0005AF5E
0027: 13 00 25 D8 02 Heap(19, 0) offset: 0005B04A
0027: 14 00 83 D8 02 Heap(20, 0) offset: 0005B106
0027: 15 00 6C DA 02 Heap(21, 0) offset: 0005B4D8
0027: 16 00 8C DA 02 Heap(22, 0) offset: 0005B518
0027: 18 00 E9 DA 02 Heap(24, 0) offset: 0005B5D2
0027: 19 00 1A DD 02 Heap(25, 0) offset: 0005BA34
0027: 1A 00 4C DD 02 Heap(26, 0) offset: 0005BA98
0027: 1B 00 9A DD 02 Heap(27, 0) offset: 0005BB34
0027: 1E 00 DC DD 02 Heap(30, 0) offset: 0005BBB8
0027: 20 00 C3 DE 02 Heap(32, 0) offset: 0005BD86
0027: 64 00 EF DE 02 Heap(100, 0) offset: 0005BDDE
0027: 69 00 54 DF 02 Heap(105, 0) offset: 0005BEA8
0027: 6E 00 9C DF 02 Heap(110, 0) offset: 0005BF38
0027: CD 00 1F E0 02 Heap(205, 0) offset: 0005C03E
0027: FF 00 4C E0 02 Heap(255, 0) offset: 0005C098
0027: 6D 03 B9 E0 02 Heap(877, 0) offset: 0005C172
0027: 99 03 F2 E0 02 Heap(921, 0) offset: 0005C1E4
0027: 9A 03 1F E1 02 Heap(922, 0) offset: 0005C23E
0027: 9B 03 A5 E1 02 Heap(923, 0) offset: 0005C34A
0027: 9C 03 24 E2 02 Heap(924, 0) offset: 0005C448
0027: 9D 03 9B E2 02 Heap(925, 0) offset: 0005C536
0027: 9E 03 FD E2 02 Heap(926, 0) offset: 0005C5FA
0027: 9F 03 25 E3 02 Heap(927, 0) offset: 0005C64A
0027: A0 03 49 E3 02 Heap(928, 0) offset: 0005C692
0027: A1 03 03 E4 02 Heap(929, 0) offset: 0005C806
0027: A2 03 42 E4 02 Heap(930, 0) offset: 0005C884
0027: A4 03 71 E4 02 Heap(932, 0) offset: 0005C8E2
0027: A5 03 A0 E4 02 Heap(933, 0) offset: 0005C940
0027: A6 03 BE E4 02 Heap(934, 0) offset: 0005C97C
0027: A7 03 F8 E4 02 Heap(935, 0) offset: 0005C9F0
0027: A8 03 2B E5 02 Heap(936, 0) offset: 0005CA56
0027: A9 03 94 E5 02 Heap(937, 0) offset: 0005CB28
0027: AA 03 DF E5 02 Heap(938, 0) offset: 0005CBBE
0027: AB 03 FD E5 02 Heap(939, 0) offset: 0005CBFA
0027: AD 03 18 E6 02 Heap(941, 0) offset: 0005CC30
0027: AE 03 4E E6 02 Heap(942, 0) offset: 0005CC9C
0027: AF 03 6C E6 02 Heap(943, 0) offset: 0005CCD8
0027: B0 03 49 EA 02 Heap(944, 0) offset: 0005D492
0027: B1 03 79 EA 02 Heap(945, 0) offset: 0005D4F2
0027: B2 03 A5 EA 02 Heap(946, 0) offset: 0005D54A
0027: B3 03 C0 EA 02 Heap(947, 0) offset: 0005D580
0027: B4 03 F6 F3 02 Heap(948, 0) offset: 0005E7EC
0027: B5 03 B0 F8 02 Heap(949, 0) offset: 0005F160
0027: B6 03 DA F8 02 Heap(950, 0) offset: 0005F1B4
0027: B7 03 3C F9 02 Heap(951, 0) offset: 0005F278
0027: B8 03 67 F9 02 Heap(952, 0) offset: 0005F2CE
0027: B9 03 2C FB 02 Heap(953, 0) offset: 0005F658
0027: BA 03 55 FB 02 Heap(954, 0) offset: 0005F6AA
0027: BB 03 C7 FB 02 Heap(955, 0) offset: 0005F78E
0027: BC 03 F0 FB 02 Heap(956, 0) offset: 0005F7E0
0027: BE 03 11 FC 02 Heap(958, 0) offset: 0005F822
0027: C1 03 1A FC 02 Heap(961, 0) offset: 0005F834
0027: C3 03 39 FC 02 Heap(963, 0) offset: 0005F872
0027: C4 03 62 FC 02 Heap(964, 0) offset: 0005F8C4
0027: C7 03 89 FC 02 Heap(967, 0) offset: 0005F912
0027: C8 03 AF FC 02 Heap(968, 0) offset: 0005F95E
0027: C9 03 D3 FC 02 Heap(969, 0) offset: 0005F9A6
0027: CA 03 ED FC 02 Heap(970, 0) offset: 0005F9DA
0027: CB 03 14 FD 02 Heap(971, 0) offset: 0005FA28
0027: CC 03 3C FD 02 Heap(972, 0) offset: 0005FA78
0027: CD 03 63 FD 02 Heap(973, 0) offset: 0005FAC6
0027: CE 03 8B FD 02 Heap(974, 0) offset: 0005FB16
0027: CF 03 9F FD 02 Heap(975, 0) offset: 0005FB3E
0027: D0 03 C4 FD 02 Heap(976, 0) offset: 0005FB88
0027: D1 03 1C FE 02 Heap(977, 0) offset: 0005FC38
0027: D2 03 5C FE 02 Heap(978, 0) offset: 0005FCB8
0027: D4 03 B0 FE 02 Heap(980, 0) offset: 0005FD60
0027: D5 03 D8 FE 02 Heap(981, 0) offset: 0005FDB0
0027: D6 03 25 FF 02 Heap(982, 0) offset: 0005FE4A
0027: D7 03 2E FF 02 Heap(983, 0) offset: 0005FE5C
0027: D8 03 81 FF 02 Heap(984, 0) offset: 0005FF02
0027: D9 03 CC FF 02 Heap(985, 0) offset: 0005FF98
0027: DA 03 E4 FF 02 Heap(986, 0) offset: 0005FFC8
0027: DB 03 10 00 03 Heap(987, 0) offset: 00060020
0027: DC 03 B6 00 03 Heap(988, 0) offset: 0006016C
0027: DD 03 04 01 03 Heap(989, 0) offset: 00060208
0027: DE 03 29 01 03 Heap(990, 0) offset: 00060252
0027: DF 03 5E 03 03 Heap(991, 0) offset: 000606BC
0027: E0 03 AF 03 03 Heap(992, 0) offset: 0006075E
0027: E1 03 71 04 03 Heap(993, 0) offset: 000608E2
0027: E2 03 8C 04 03 Heap(994, 0) offset: 00060918
0027: E3 03 20 06 03 Heap(995, 0) offset: 00060C40
0027: E4 03 85 06 03 Heap(996, 0) offset: 00060D0A
0027: E6 03 D7 06 03 Heap(998, 0) offset: 00060DAE
0027: E7 03 A4 07 03 Heap(999, 0) offset: 00060F48