Fallout 3 help! quests dissapeared?

i own fallout 3 and fallout 3 GOTY edition when i attempted to play mothership zeta it always froze on the GOTY version so i tried playing it on my original copy but then the GOTY edition quests went away along with a couple of my weapons. i quickly put back the GOTY edition in and restarted my ps3 when i loaded my data the mothership zeta,point lookout, operation anchorage, the pitt, were back but im not sure if broken steel is back even though i previously finished two of the broken steel quests and my weapons were gone along with a couple of broken steel quests i started such as "Protecting the waterway" and i can no longer start this quest because the person i need to talk to to start the quest is no longer at rivet city. does anyone know how i can regain what i have lost?