Clarification of earlier comment: there are actually differences between the vote files, but I didn't see any differences in the results.
In particular, especially with Senate candidates, there appear to be more rankings in this file. From what I can gather by looking at just a few of the differences, it looks like the new file includes people who were dropped before tabulation.
You can view the differences yourself by uploading each file here:
I think the vote counts are actually the same if you pre-drop the pre-dropped candidates. The only difference is the one vote from the paper ballot. So the find-and-replace methodology worked fine, it seems.
Given that he is the webmaster, I don't think anything's off. You could perhaps argue that Yaman shouldn't be the Elections Council webmaster, but folks aren't exactly breaking down the doors to work for the ASUC.