I had the exact same thing happen to me. I discovered that I had media missing. I had about 275 media files what went missing while uploading. After several days of replacing the missing media from my External Media Vault, I tried once more. This time it worked about half, still missing media, most likely it did not finish the media processing. Then I noticed that in my FTM program that about 25% of photos were replaced with another media file from that person.
After fixing my FTM file, I deleted my tree from Ancestry and uploaded again. This time it worked and I saw no unnecessary changes in my FTM program. I have about three thousand media files and it took a very long time to upload them. This was all after the FTM upgrade along with a great slowdown of the entire program and many crashes frequently.
At least I have not had any major problems for several days.
I am still sure that they will get this fixed.