Only just started playing crysis 2 SP and got to the second part were you collect some keys next to a body and the first time they were there but I had to exit the game so the next time I reloaded my save game the keys are not there.

Is there a workaround for this and what are the Souvenirs, Dog Tags, Car Keys for anyway

They're collectibles that unlock bonus features like concept art. You only need to collect them once, after that, they disappear.