How to get rid of error messages after second try where file was uploaded successfully?
There is a working patch for this issue here. (File validation error message not removed after subsequent upload of valid file - 1792032)

That patch issue is waiting on someone to write tests before it can be RTBCd. It shouldn't be hard to adapt that patch to Drupal 7 in the mean time. Just make sure you document the fact that you have patched/modified core somewhere for future developers.