Just got an email from Tim @ Member Services. He was able to fix my issue with sync/linking to ancestry.
Go to File and click on "New" it should show what trees you have listed with ancestry.com.
make sure to check the box "Link to Ancestry" and then click on "download" next to the tree you want to download - give it a name so you don't confuse it with your existing tree.
I'm back in sync again!