So, I have a torrent that I created with a big number of files so it must be complete because I created the torrent.
When everything is in its original place, all files show up as 100% complete, as they should.

After removing some files from the folder (because I do not wish to upload those but also I don't want to create a new torrent), other files that have not been removed suddenly show 92-97% completion.

So: removing some complete files from a complete (self-created) torrent causes other complete files to suddenly appear incomplete -- and they are even downloading parts from the leech that was supposed to be downloading the torrent from me to complete these newly incomplete files.

I have no idea how this has happened and if it's a problem with Tixati or my drive's file indexing or what.

when you removed the files, you removed some of the pieces that overlap between files, which will make those file incomplete. you should have turned off the files in tixati and then deleted them in tixati. that way you will keep the overlapping pieces.

Another way of putting it is the .torrent file is a 'blockchain' of verification for the torrent, and the blocks are large so more than 1 file can end up in a single block's verification. When Tixati goes to verify the validity of the torrent, because a couple of the files that generate the appropriate hash do not exist, all those blocks will completely fail, and some of the other complete files on your drive are partially within those blocks. End result, the torrent client can't calculate the correct hash for that block because data is missing, and because some of your still-there files have a portion of their 'hash' in those blocks, those 'confirmed' parts vanish from the other files, giving your 90%+ completion numbers. The torrent client simply cannot confirm the validity of those 10% gaps in the files since the rest of the data needed to calculate the hash is missing.