Seems like you are attempting to expand the Tinderbox approach and apply it to files, rather than text notes. As @mwra and @Bernard-0 indicate, this is not workable.
Really speaking, this is a file management issue. There are dozens of blog posts on the web that address various approaches to dealing with data file proliferation and bloat - all of them acknowledge that the job demands effort, trial/error, and consistent housekeeping practice. There’s not a “one size fits all” solution out there.
You could look into EagleFiler for organizing files, as it handles a wide variety of file formats and annotation. You might also just use a good zip application like BetterZip to bundle a bunch of files, and peruse the contents later without needing to unzip the sets. Good luck.