If you lose your achievements on Quake 4 because your profile was corrupt (e.g. from playing several levels of Quake 4 with your entire Profile and Gamertag at a friends house), you need to do two things as well as be smart enough to have saved the game a lot before you lost the profile.
One, recover gamertag on your own Xbox 360 using the gamertag recover icon.
Second, once you have recovered your Gamertag you will notice that you have lost all of your acheivement points since playing Quake 4 or any other game at a friends house. At the Quake 4 start up screen pick LOAD game. Find a level which was close to completion. Select Load Level.
Play the level and you will obtain the achievements as if you played the game from the beginning (I loaded a game where I was near the end of Act 1. Walked into the EXIT and I had an achievement blink onscreen).
I was lucky in that I saved a lot.
I was able to recover my used weapon to finish a level Achievement because I saved those levels before I exited. Lost my gamertag. Recovered it. Loaded those saves and got my achievements back after only 1 second of gameplay.