Sharing my experience trying to retrieve my lost files, upset and frustration to describe this latest Apple mess, how can they release a product of such quality, it's beyond me.
Anyway in my case, I lost all my Safari Bookmarks and could not find them anywhere, even going thru the bookmarks.plist in the Library folder.
Contacted Apple Support, initially they got me login to the iCloud, there is a restore function in the iCloud, it seems that Apple knows of this problem, I could see that for whatever reason, Sonoma unilateraly deleted all my Safari Bookmarks without warnings, it indicated that it was deleted a couple of hours after I upgraded to Sonoma (big regret - another story).
The normal Apple Support was unable to help, they got a more senior guy to call me back, and helped me do a Restore from my TimeMachine backups that was (in my case) 4 days earlier. Oh by the way, he got me to disable the iCloud sync for Safari before restoring, however every time you turn it on, Safari will revert back to the one copy of Bookmarks in the iCloud. Somehow the iCloud Bookmarks takes and replaces whatever bookmarks I have on my Mac, **** frustrating. So finally I have to disable the Safari Sync on iCloud then I can have all my previous Bookmarks, as soon as you turn it on, the bookmarks will change to some random bookmarks on my Safari, and what is strange is that those are only bits of my own bookmarks the rest I am not sure where they came from, I guess could be the Safari default bookmarks.