I ran into this issue too today. I had named a few notes with a leading dot to keep them showing at the top of the list, because using an underscore for this purpose turns following text to italic in the editing pane. Visually this is confusing. Then next time I opened Obsidian, they were gone from the note list (and from the Mac Finder). To get the files back, I had to recover them from a OneDrive backup, but then the links to them didn’t automatically update, to I had to manually search and change every instance. I know not to use dots now; just providing the info for consideration in the update process. (Also, I still don’t like the side-effects of using underscores.)