leaking from roof around chimney
It is dang near impossible to tell where and how it is leaking site unseen. I know you probably have but, take a flashlight up in the attic and look for water stains, remember water will run down, across, drip, and the leak may not be right above where you see the damage in the house. May not even be around the fireplace. See if you can't pinpoint the exact location of the leak instead of generally calking. Look at the rig row(very top shingles) and make sure none were cracked from bending or steppng on.(do not step on the rig row). If all else fails, you may need to get one more opinion.
You could also try having someone on the outside(maybe even on the roof) spraying with the hose from all different angles(but not up, simulate rain) and someone in the attic with a light to see if you can't pinpoint the leak. You really need to pinpoint the leak before you can fix it. And like I said, it is possible it may not be the fireplace.
Hope this helps.
IF you are going to have to replace any rock from the damage you may try cutting out the piece to replace then do the water hose and looking like that. You cannot however (not recomended) replace the rock until the leak is fixed.
In any case, I hope your roofer is successfull!