I wasn't able to upload an updated resume the last time the hiring window open, and I brought fresh resumes to hand to the interviewers. They asked why my times were so different between the current resume and the one I had online. I told them that I had an app on file for some time and wasn't able to upload a fresh resume during this window. The HR interview told me that if that happens again in the future, I should contact them and they will remove the previous uploads and make room for new stuff.
This was just my experience with that. I agree that it would be a nightmare for them to do this for the scores of apps that they get, but it sounded to me like it's something they do often.