i had a similar problem going over a few months at work, and I totally understand the OP's frustration.
OP - I don't know how you can get it resolved, but in my case, work requires that I complete professional training. About six months ago they started to roll out content on a new system, and I always completed the training within the week (we were given up to a month).
I had major issues completing the training on a work computer (sound problems and there were no transcripts of the training content), eventually spending quite a few hours on the call to an IT Helpdesk. I got it sorted every time, did the training (about half a day per module, multiple modules). I often did it in the evenings and on a couple of occasions at weekends to get the problems sorted.
then, when the final big "milestone" compliance audit was taken, my name was on a "not compliant" list which was distributed to Heads of Department. it was mortifying. I raised it as a problem with our learning team, and they basically told me to just get the training completed as they had no record of it.
I could provide dates and rough times that i'd reviewed the content/did the assessments, but it was a case of "computer says no". i couldn't have literally fitted all the missing training in by the "final final deadline" they gave as an ultimatum.
I ended up in such a stressed, tearful state that I basically refused to re-do the whole lot and told them to take it up as an HR disciplinary matter, and copied in my head of dept.
a few days later i got a short sorry email from the learning contact saying there had been a few people with the same problem, and it was some issue where the new system hadn't "linked" correctly with our employee records.
i still get stressed and anxious when i think about it now, and i didn't even have to re-do all the work! even reading your post made me feel like i did when no one at work was even trying to help figure out what had gone wrong.
so, this isn't helpful to you OP but i totally, totally sympathise, it's a rotten situation. do you have a manager who's easily available/can force them to check their audit records/something else which means the onus isn't all on you to sort out their problem...?