Thanks to @arraybolt3 I was able to fix the issue. Honestly I overreacted when the website I was using was able to change my settings and bookmarks, it shouldn't be able to do that without a good prompt from the browser and outside of the website view....
Also Firefox Sync didn't *replace* my bookmarks anyway, but *merged*.
That said, my settings are still messed up, but thankfully my carefully created site cookie whitelist wasn't deleted from. So there's that!