Blizzard's customer service is without a doubt, hands down, the best for any game I have ever played. No other game I have ever seen has a GM team of this magnitude and helpfulness. Some people just have ludicrously unrealistic expectations of them- not meaning the OP here- but it is important to bear in mind that we are spoiled by having these people on hand to help us where most games have just a forum or nothing at all.
Last week when I had a problem where I needed this kind of service the GM suggested resetting the instance for me this was of course BWL (very old content) but I told him no because I couldnt use a reset for anything, I just wanted Nef as I can solo him. So it is possible and they could even go as far as removing VP + loot from the previous kill and just letting the players get another try on the achievement.
Even if they have one shot spells, I don't think that using them in that way to fix the number of bosses that are up in a raid would be acceptable within their power use. Doing that, the GM would have probably been reprimanded by Blizzard. Just because someone has the power to do a work around for a fix does not mean they would be right in using it.
Yes GMs can 1 shot stuff,... you'll never see them do it because they'll loose their little job but they can (ie... anyone remember martin fury?)..
but besides that GMs can definitely track all this stuff from even months before and on top of that, can see a log of achievements that are NOT in your achievement history that you SHOULD have. The reason I know this is because the scumbag GM i keep getting to replace my EPIC (and i mean EPIC in the strongest of senses) mounts from vanilla says... "I know you had X mount and X mount, (etc.... ) but we cannot replace mounts after server transfer/faction change on new servers that never saw those mounts ... :-/
Funny cause I'm fairly certain I met a guy with the exact mount I'm specifically referring to who told me they gave him the same runaround and eventually the GMs GAVE IT TO HIM!! He told me to keep pestering them and ignore their threats about banning me (haven't been banned for spamming them yet in about a year) So I'm freaking screwed.... but to the point... yes the GMs can see that you SHOULD have an achieve (some flag in their program goes off or something) and are able to grant IT and the same is true with mounts (even pre-WoTLK stuff evidently as this GM told me). If I were you I'd make them suck it up and slam them with requests, just keep requesting. They threaten to ban me all the time but can't because they know its a legitimate request, it's their own damn problem if they don't want to fix it. Unfortunately sometimes you get stuck with 1 GM 100% of the time and then you're screwed like me but luckily they aren't all reading some dumb paper that tells them what to type everytime so if you get lucky (and another GM) you might have your problem solved.
bleh /rantoff
It is a shame, but this is life i'm afraid.
I understand your frustration, I really, really do as i've been there before when Champion of Ulduar was removed. The night before the removal, we where not rewarded it despite meeting the criteria. Response was the same.
Meh, its just a achievement and a very outdated one at that. I myself have never had a problem like that but haven't gone back to do outdated content neither.