Try running Places Maintenance: https://addons.mozilla.org/en-US/firefox/addon/places-maintenance/

I don't use Sync, but could you clarify how these appear?

For example, your Bookmarks menu has duplicates at every level/in every folder, which would sound like corruption.

Or your Bookmarks Menu has new folders which refer to desktop or mobile bookmarks where you find a full copy of your normal menu. That sounds like a problem that probably could be cleaned up with a de-duplication add-on of some sort, but preventing it from happening again may involve addressing some database corruption.

Where do I find a De-Duplication add on?

You could search here:

https://addons.mozilla.org/firefox/extensions/

Since this is sensitive data you don't want to lose, I suggest comparing reviews for several different extensions.