Which comes 1st, the mold remediation or the re-application of drylock on old stone walls?
I've never used drylock, but have had good results using kilz, which seems to be a similar substance. The paint itself kills mold. On stone, I would use the oil based kilz after a thorough cleaning with bleach. Before applying, heat the space long enough to assure that everything is very dry.

Kilz seals the mold from entering the room. It also penetrates brick, block, and maybe even a little into certain types of stone.

Regarding duct work, and anywhere else the mold may have parked itself, it's important to clean/replace anything showing mold before applying kilz, because doing any work on ducts after the application will stir up mold again.

Wear a mask!