Second time I’m experiencing this same problem. I woke up this morning to my entire vault being empty without explanation. The only note that is available is the one that was last open/being worked on.
iCloud Drive folder which contained all notes is also empty aside from last file.
I haven’t had issues with iCloud but I also sync to a git repository each time I finish working in Obsidian just to be safe. You may want to explore doing this – it’s pretty easy to do.
Here’s a good example of doing it, although I don’t use the crontab portion of it because I prefer to manually sync each time I’m done.
This is tough to debug, sadly.
Is there anything else that might be acting on this folder except for Obsidian? Other apps or automations, perhaps?
This help article might give you a restore route: https://www.howtogeek.com/400918/how-to-recover-deleted-files-from-icloud-drive/