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Some different things would happen depending on various maintenance timers. The client does not constantly monitor its file store, and it only ever accesses a file when it needs to do something with it like showing it in the media viewer. It does not rescan a file when it loads it.
If a file were to change, the client will try to load it with its current understanding, so if you swapped one jpeg for another with a different resolution ratio, it would probably draw it ok but all stretched to the wrong size canvas. It wouldn't lose the tags for those files, as tags and so on apply to the db store's understanding of the file, which is still all correct for you. It might sperg out if it needed to generate a thumbnail or something else clever.
A problem would come if hydrus ever did file maintenance on those files. It would recognise the files had changed in terms of bytes and throw some errors, and probably remove the file and put it in a 'missing_and_invalid_files' directory in your install_dir/db directory. Maintenance can be triggered by things like thumbnail resizes gone bad, so I expect these weird files would get looked at eventually.
I recommend you make a copy of those thumbnail folders, just in case you want to try something clever with them later. Then get the client going with empty file folders and go database->maintain->file maintenance->review scheduled jobs and then add a 'check if file is present in file system' for a 'system:everything' search. Force it to do that job, and it'll clear itself of the missing records and export all those files' known urls to that 'missing_and_invalid_files' directory. There will be a 'all_urls.txt' masterfile, which you can open, copy-all, and then paste back into a 'urls' download page in the client. The client will then download all those correct files again. This will make for a more 'correct' db and get you nice files again. It would not work well if most of your files were not downloaded and do not have nice known urls.
If you wanted to have thumbnails in lieu of the files, it is probably safer just to import those thumbnail files, although they won't get the tags of course. There's the slightest chance that your png thumbnails will be the same file as the original png, but I can't say that with confidence.
Let me know how you get on here.