I managed to clear my phantom tabs (again), but I also have another problem: bookmarks and reading list have stopped syncing entirely. (The last time I had phantom tabs, bookmarks and reading list also stopped syncing. However, after I fixed the phantom tabs, syncing resumed normally.)
With Advanced Data Protection off, my bookmarks and reading list are ”frozen” at a specific point in time (roughly two weeks ago when the phantom tabs appeared). No matter how many times I delete the bookmarks manually and toggle iCloud syncing for Safari (whether opting to delete the local copy or not), those same bookmarks reappear the next time I enable syncing.
I have completely logged out of iCloud on every device except my two iPhones (because re-adding all my Apple Pay cards is a pain), but I will try logging out of those later.
If I try to view deleted bookmarks on iCloud.com, it just says “loading” and after a while says there are no bookmarks.
What happens with Advanced Data Protection enabled is even more frustrating. With ADP enabled, the frozen-in-time bookmarks aren’t downloaded at all. (I get zero bookmarks.) If I try to load my bookmarks.html and then edit them, Safari reports that they are still syncing. However, syncing never finishes (or even appears to start), and Activity Monitor shows no activity for SafariBookmarksSyncAgent. Restarting the agent does nothing. I have deleted every identifiable file and keychain entry related to bookmarks and even reinstalled macOS to no avail.