Cool idea! First, how did you "thin" your campaign file to begin with? I'm guessing you used a CASC editor and extracted all the imports to your local files directory and deleted them from the campaign? Did you delete the imported files via the CASC editor, or did you use the world editor and delete the individual imports?
Ladik's MPQ Editor to delete folders from MPQ campaign file, and occasionally mpqmaster because the former sometimes messes up the campaign file (making dummy change with mpqmaster fixes it) while the latter can't delete folders. Yeah, I know...
And are you deleting the assets from the campaign file or from the individual maps? (or both?) Are most of your imports imported at the campaign level, or are they imported into each map individually?
From the campaign file. I have very few imports in individual maps, mostly AIs and single texture, tile etc. overrides, so they don't bother me.
My thinking is that if you deleted the assets from the campaign file but left the import list as-is. The import list is stored as a war3map.imp within the map/campaign itself and is a simple list of assets imported into the map. My best guess is that when the editor is building the archive (e.g. the w3n or the w3x), it will look at the import list and then it'll "search" for each file (which I'm guessing will look first within the map archive itself and then look within the local files directory) before packing it all up into the final archive. But I haven't tested it.
If my theory is right, then to get your workflow working you'd probably need to remove the imports from the actual import list too. But it probably would kinda suck to have to manually re-import everything down the road, trying to get all the paths right. But some simple scripts could maybe smooth out the process there. Regardless, I'd recommend making a back-up of your campaigns/maps as-is first--and once I know your process maybe I can make some more specific recommendations!
Well, someone on Discord adviced me to remove .imp file.
For some reason removing it didn't work on my main campaign yet (somehow import list gets recreated), but it did on a clean one, with a single map and a single local file import. I imported it to the campaign, created a copy under Warcraft III\
retail\war3campImported\, cleared .imp file, relaunched the campaign - the import's still working, it is not saved into campaign file, and import tab is empty. So far, so good.
EDIT:
Okay, it did work with main campaign, by mistake I extracted .imp backup into retail folder

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EDIT2:
Okay, so far everything works smoothly from local files and campaign/maps save time went down drastically. So it's great for work on missions. Now I need to work out a flow of making changes that involve the imports. I believe I'd have to restore .imp file, add/modify imports, then export them to local files (or just make the same changes) - but I need a modified .imp file, so I need to save the campaign - which would produce "fat" file again... Ehhh... Damn, I'll just write a script to scan local files and generate the .imp file for me.
I'd also need my imports back whenever I want to use a sound because imported sounds are fetched from imports and they're gone without the .imp file.