Do all your devices which are connected to Sync always stay connected to Sync? Or are you enabling Sync per device when you feel like it?

I ask because a desktop / laptop device that hasn't been connected to Sync or used for quite awhile would have the old, deleted bookmarks and when first connected back to the Sync server it is possible that the initial Sync event went askew.

The Sync server sure as hell wouldn't keep 4-6 month old bookmarks around, so the answer is a device that hasn't been used or hasn't been connected to the Sync server in quite awhile.

Duplicated bookmarks is indicative of corrupted bookmarks. The "fix" for that is to Disconnect Sync on a laptop / desktop device and then open Help > Troubleshooting Information and scroll down to Places Database and use the Integrity > Verify Integrity button and wait for the results chart to appear. Then view the results.

As far as the "base cause" goes, I blame it on "mobile devices" Sync - namely Firefox for Android and/or Firefox for iOS, along with a Sync user who may have also used the iCloud Sync extension. I have researched the support threads here and I feel the start of weird Sync issues which seemed to have began 4 1/2 years ago when the Sync feature was modified during the latter Beta stage of development with the Firefox for iOS app - like in May or June 2015. Only users who have connected a "mobile device" seem to have the "duplication of bookmarks" fault; in a few cases it was dozens or even over 100 sets of duplicates for users who were slow to catch on that there was a problem. I am hoping that this "mobile device" issue will be solved shortly as Mozilla releases new versions of the Firefox mobile web browser app.

In conclusion, if you try to manually repair the 'carnage' by all means dis-Connect from Sync on the laptop/desktop devices before deleting any of the duplicate sets of bookmarks. When still connected to Sync the problem just may get worse; like a 'whack-a-mole' game from what I have seen posted.

And before re-connecting any devices to Sync reset your Firefox Account (FxA) password to clear the corrupted data from the Sync server.

the-edmeister thanks for the super complete reply.

I keep both devices synced at all times, or at least as far I'm aware of. Now that I remember, three days ago FF on Android asked me to login to verify my email, can't remember exactly. I did it and added a secondary email as well. But I did use my laptop and mobile device right after that and didn't have the new bookmark added. They appeared today right after I added three new bookmarks in my laptop.

the-edmeister said

In conclusion, if you try to manually repair the 'carnage' by all means dis-Connect from Sync on the laptop/desktop devices before deleting any of the duplicate sets of bookmarks. When still connected to Sync the problem just may get worse; like a 'whack-a-mole' game from what I have seen posted. And before re-connecting any devices to Sync reset your Firefox Account (FxA) password to clear the corrupted data from the Sync server.

I already deleted all the duplicate bookmarks, ha. I did just export a backup of the current bookmarks in case there is still some strange behavior in the next couple of days.

I will follow your recommendations if that does happen, thanks again.