Ah yes, I remember the discussion of that option a few years back -- I was kinda hoping there'd be a way without me substantially altering my workflow. Toggling the "Manage resources as patch files" has some pretty serious consequences that I wasn't looking to implement at this stage.
I'm using Kawa's build v3.2.3.0, btw.
Toggling it on has a fairly lengthy pause while it extracts each resource to an external patch file -- not sure if it overwrote any existing patch files with their (older) internal resource counterpart -- also not really sure if there were any overlapping files there... it's been nearly a year since I touched this mod.
Once all the patch files were extracted, the Explorer only showed patch files, not any files already existing in resource.000. But Tools-->Rebuild resources seems to have worked as I'd wanted.
Trouble is when I uncheck the "Manage resources as patch files" to change things back to how I had it before, it's asking me for confirmation after it deletes every single script file. It also asks if I want to delete the corresponding script source code (thank goodness that's not checked by default).
I'm just going to hard-crash SCICompanion and restore from the zip I made beforehand -- I don't feel like clicking yes on 285 individual confirmation dialogs tonight. It'd be really nice if the Rebuild resources window itself could just build those patch files in without needing "Manage resources as patch" enabled.