Some things you might try (I’m just spitballing):
- Make a copy of your vault folder and open it as a vault in Obsidian. Does it have the same problem?
- (After backing up) Try deleting or renaming config files 1 by 1 and restarting the app (I think Obsidian will regenerate ones that are missing, but you may want to research that). Does the behavior persist?
- (After backing up, of course) Try removing other files 1 by 1, in case Obsidian is for some reason hung up on indexing one of them. As a first rough cut, you might remove all non-Markdown files, and if that has no effect put them back and try removing all Markdown files. If 1 of those does something and you have folders, you could get more granular by removing folders 1 by 1.