I am using iCloud to synch everything. Trouble started when I was suddenly getting older bookmarks on my MacBook. I run Windows in a VM on my iMac, which I had been working on just prior to the mess. iCloud synch was also set up on Windows, and that is where the "pollution" came from.
Problem is, I never thought to disable iCloud synch on the VM before I cleared out favourites in Windows. The Bookmarks Menu on the Mac side, was damaged by removing that same named folder of Favourites in Windows.
I really don't want to tackle moving a boatload of stuff into a new user at this point. And I do know that would cure this weird little glitch, but I hope it can be fixed in another way. I may try using iCloud.com/Settings/Restore to see if an older archive will fix this mess.
Weirdly, the Bookmarks Menu folder shows up when you hover over the left end of the URL bar, then click and hold that little icon (circle with + inside). So it is gone in most places but not that 1 spot. See screen cap.