Hi Tyson,
Despite, it sounds logic and correct, I can positively confirm, that it's not always sufficient. Had just the same issue. Despite repeatedly overwriting ....After upgrade from 4.2.2 to 4.3, I still had roughly 100 files from 4.2.2 left.
A comparison with meld between the live files and a fresh downlaod was the proof and the fix, as well as dozens of errors and little problems gone, within the first minutes of testing