Well I kinda just told you.
The only option you have, to be on the safe side and not make your game crap out, is to save the "altered" file under a new name, go into ued and compare to the original UT pack and see which have been altered or renamed, and then erase the altered pack and save a mylevel texture for the ones changed and use the EXACT same name that was in the altered pack.
For example. Say i Have "Mine" utx and some asswipe named Steve47 made a map that had "Mine".utx included in the map zip, only he altered stuff and saved. the pack. Steve 47 is a bitch, but you can solve this problem by taking the tex pack in his zip, renaming it "SteveIsAnAssHolio" and putting that in UT texture folder. Then open ued and open his map, and open that texture pack of his pack and then open your original Mine.utx file and compare. Now say he added three new textures because Steve47 is stupid. Remember the name of the 'added' files, export them from the new altered pack, then reimport into a New texture package which you MUST name "MyLevel' Import those new altered textures u just exported, using the same name, and DO NOT save MyLevel as a new utx package. ALL YOU HAVE TO DO NOW is save the map and close ued.
If this doesn't work, you can either.
1) Overite your old file with his, and possible fu<k up UT.
2) Call it quits, don't hassel yourself and just go play DM-Amon instead
Now before you do ANY of the things I mentioned, just to be on the safe side in case it really is YOUR system that is fuggered (you can deny it all you want, but sometimes the problem is you and you dont even know it, trust me) and reinstall UT and the newest patches. Then try again, if still F'd up, try my method.