There are plenty of files within .obsidian which are supposed to have different content on mobile and desktop. This could be plugin settings and/or source, various configuration stuff, metadata/cache information, and so on.
I have .mobile, .windows and .linux config folders.
Sometimes when I make changes to the whole vault (like alias > aliases and other changes), I relaunch as .obsidian, which makes reindexing much faster, then relaunch again with .mobile. My files were indexed, good. So one can play around with the config folders.
This trick did not work on PC, though (I mean the reindexing started from afresh upon relaunching the second time).
They will likely come back occasionally. Especially if you are using Obsidian at the same time on multiple computers. This happens with other cloud tools like Dropbox. I get conflicted workspace files often in Dropbox. I just delete them and move on.
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