I am having almost the exact same problem. My tree was suddenly unlinked. I had no choice but to re-upload the tree to a new file on Ancestry. After waiting overnight for it to upload, I now have two trees on Ancestry. One linked and one that thinks it's linked at Ancestry, but doesn't on FTMM2.
Like you, now it wont let me synch, saying to try again later. Maybe it's just an overload on the servers, but who knows.