I tried searching for anyone else with this issue a month and a half ago, because this happened to me. The bookmarks I lost were not all nested, and I've notice this happen in windows 11 (all exploit protection disabled), and debian 12(both OS different browser profile) I wondered if maybe using the 'Exit' in menu instead of X/middle click tab to close might be related, but I don't know any code evidence in recent releases to corroborate this. This issue was first recognized for me about 2-3 firefox versions ago. 32gb ram i9 9th gen, I use privacy badger, privacy possum, adguard with most filters enabled, decentraleyes, and user agent switcher. I always run in private browsing. I don't think this is related to a malicious website.

I do not have any sync agents like firefox sync enabled. One instance has about 50~ bookmarks with 3 folders no subfolders, one instance has about 500 with many subfolders.

I assume only recently added bookmarks have disappeared, but I have no way to verify and my memory wasn't perfect.