"What I dont understand is Ancestry's disinterest in clearing up these issues."
I don't know that Ancestry is uninterested in resolving these issues, but their support system is geared toward correcting user-error and ignorance. I'm afraid they're just not very well equipped to deal with software bugs and other quirky software issues. For future reference, you might try coming here first for assistance from other users in the community.
I feel your pain of a linked tree that won't synchronize. It's happened to me not a few times, and I've lost countless hours of work each time because FTM and AMT don't fully synchronize. I hope you get your broken sync fixed somehow and don't have to suffer that yourself.