You'll want to read this reply.

""What precisely does “sync” mean with respect to transferring Firefox information between devices?" https://support.mozilla.org/gl/questions/1379470

This talks about sync FAQ https://support.mozilla.org/en-US/products/firefox/backup-recovery-and-sync/sync-data

You'll want to read this reply.

Neither of those seem to mention extensions/addons though, especially not disappearing. It's mis-syncing.

I recommend you log both system out of sync and go back to the working profile and copy that back to the computer and change the password. Doing this will insure that data on A will copy over to B computer and nothing will get wiped out when you login with the new sync password. Sync will remove or update based on the Sync A computer to B computer and if they don't match depending what profile you copied back it will use that data to sync A computer to match B computer. This is my understanding of sync changing password help to reestablish the sync to match A computer and not B computer changing the data. But sometimes if B computer doesn't update you have to let it stay sync for the data to sync to do a proper update so both match. I don't guarantee this will work but at least this mean one isn't overriding your sync data with the wrong data.

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Not sure why someone downvoted you, this seems like a decent thing to try. I ended up just fixing it all manually, but if it happens again, the sign out and password change option seems worth a go.

Yeah not sure why people get ants in their pants. But if one thinks logically this is what I would do if I used Firefox sync to make sure they aren't duplicate or the wrong data is updated rather then the data you need.