So glad I found this thread.
I have been having the same problems over and over again. Ater trying everything that was suggest, unlinking, redownloadinging, etc, I am left with just my tree on Ancestry.
Yesterday I tried to create a gedcom file on ancestry and it is stuck at 16%, I have tried everything that support suggested in the end they told me it was a problem with my computer and there was nothing they could do for me. I still cannot figure out how it is my computer when the gedcom file is being created on their site. If I am ever lucky enough to get my tree loaded back on my computer, I will not upload to ancestry again.