Browsers store bookmarks inside a profile folder. If the browser opens a different profile, or a new profile is created automatically, all the familiar bookmarks vanish even though they still exist on the drive.
Sync is the second common cause. When signed in, the browser matches local bookmarks to the cloud copy. If sync signs you out, resolves a conflict incorrectly, or merges two profiles, bookmarks can move, duplicate or disappear from view.
Some cleanup tools and security suites remove browser data as part of a privacy sweep. If bookmarks disappeared after running one of these tools, it probably deleted more than intended.
The good news is that real deletion is rare. Most cases are a profile or account mismatch, and the bookmarks can be recovered by signing back in or switching to the correct profile.