In terms of calculating GPA's, it would be easier for them to just input the new grades and have the computer to easily adjust the GPA instead of having to manually check all over again the grade replacement and how the credits line up. The problem is that once verified, it is locked to keep the 'integrity of the original verification process.' Some applicants aren't doing retakes, and this would just make everyone's job easier. For those that are doing retakes, then they can start a new application process so they can reverify the whole app. It doesn't sound unreasonable to me since they're going to be scrutinizing it more carefully for those retakes.
Going forward, it won't matter anyways because they did write the instructions in the manual and it will be the applicant's fault for not reading it correctly. There is a lot of bs when it comes to being a physician when it comes to paperwork and following instructions.
Also, why would a student call over and over again to fix their problem? I did say it was silly for them to implement it without proper notice, but going forward it seems justified to me when proper notice was given. Not everything needs to be spelled out to applicants.