Thank you to all who posted regarding this issue. I have the same problem as you with the new upgrade on the Ipad2 operating system. I assumed it was because my tree was too large with over 2500 names. I have a few large photo files that I uploaded to Ancestry and assumed that may also be the issue. Before the tree disappeared completely I had duplicate names appear on the Ipad2 screen for my wife and boys.I deleted the tree and re-upped it to Ancestry. Now I have nothing after it appears to upload the files. I also wondered whether I needed to change the name of the tree as the previous upload was too similar.
It would be nice if the new version would allow for deletion of other trees as you can do with the sample tree. It would also be nice to save the file to the Ipad2 and not always need to download the tree.