According to Big L's brother, L was with some people when they went to go do something to Gerard Woodley, but it didn't work out (Kinda implied nikkas went to shoot him, but it backfired and they couldn't do it for whatever reason). So when Gerard had a chance to get get back, he remembered Big L being there, so he clapped him up.
Others say it was because they couldn't get Big L's brother who was in jail at the time (Another brother, not the same one I mentioned above). He got killed after he got out of prison, when he went to try to find out what happened to L.