If I select an object and bake lightmapping to it, every other object in the scene gets its lightmap cleared. Is there way to keep those other lightmaps?
If you don’t use Unity 4 no.
In Unity 4 you can now do this without any problems 
Ok thanks! Good that I am still at the learning stage. I just upgraded Unity to 4.0 so I tried this just now and it works as you say. Thanks.