I moved your post into its own thread because it doesn’t seem to be the same problem as Obsidian Sync on iPhone Overwrites Newer Data, Causing Data Loss (which is about new content being overwritten by old content).
I’ve never seen this problem before. Do you have any plugins that do file naming at all?
You can restore from your backups. If you don’t have backups, I strongly recommend setting some up (for all the data you care about, not just obsidian. This should make that easier: Back up your Obsidian files - Obsidian Help.
Otherwise, Obsidian’s restoration features are aimed at single files, so I think you may have to rename them manually, which will be tedious but doable (at least it’s not 2000). You may want to do it outside of Obsidian, with Obsidian closed, so it doesn’t keep uselessly changing all the links that point to those files. (Did the big renaming also change all the links to them? If not, that would be good luck.) Make sure to backup first!