I had the same issue at one time but this was only on FTW (Mac version). The ancestry tree was unaffected. This allowed me to download a new tree from Ancestry into FTW by using the File/New method. All source documents from Ancestry are transferred at the same time.
Why this all happens in the first place I have no idea. I once used the iPad App as well and this messed things up for me. This could have been finger trouble my end though.