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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!
I feel like every time I get this suddenly upset at a good or service, it ends up being an overreaction