I want to throw my two cents here!
I don't have the game, but you said your upgrades are stored in your profile? It is possible to do a similar workaround you can perform on Command & Conquer 3, I will quote the post here!
Originally Posted by Oblivion Knight
I've been asked for more details, but I'm somewhat reluctant since the same tools can be used to achieve far worse things, that some users may find tempting to exploit (and probably eventually get banned).
First thing that's bound to get asked is, "Will I get banned for doing this?".
The long and short of it is, I don't know. Technically you're not gamesaving, nor hacking achievements. You're temporarily erasing your profile's memory of ever having played this single game. Technically, it's probably against the ToS since you are, to a degree, using a tool to modify or engineer your profile. It's a very grey area; Personally I feel that Microsoft should be doing more about glitched or unattainable achievements anyway, and if they have any issues about me doing this, then they'd have a heck of a battle on their hands!
** DISCLAIMER: I will not be held responsible for any adverse affects to your profile and/or console by using this guide **
Ok, so while I'm not giving any info on the tools used, I will go in to more detail about the file you need to delete; it's contained within your profile's file (make a backup!). You need to explore it's contents and you'll discover an additional folder with the same number - 4541080E - of where the game's saves are stored (you should have backed up and deleted the saves already), I think this folder just has a single .gpd file in it.. Delete the folder, save and rehash your profile (not sure if it's needed, but just in case), upload back to your HDD and go back to your console and play the game offline. Go through as normal, and this is where you'll be prompted with the in-game notice again.
It's probably safe to sign in to Xbox LIVE at this point if you want your achievement timestamped, I did, half expecting the game to moan about a sign-in change - but it didn't. Select "no" to playing the Boot Camp, and your achievement should instantly unlock. At this point, I quit to dashboard and went to upload my backed up profile file and saves for the game. I loaded back to dashboard whilst connected to LIVE, and the achievement was still present on my profile. I also tested to make sure my GDI campaign progress loaded as normal, and it did.
So what I mean is to delete something associated with the game in your profile so it will reset the update counter.