I think the safest thing for you to do is create a new tree from your clean FTM file. This will mean unlinking the old AMT tree from your FTM file. Even safer would be to use a new clean FTM file for your new ancestry tree. No need to delete the old tree; you can use it as a reference for the new. And yes, you will have to re-do the invites, but still, having a cleaned-up tree is worth it (at least in my mind).
And keep auto-sync turned OFF.