On the engine side, run a thread tap in there using lots of cutting fluid. 1/2 turn in, 1/2 turn out as you go. This properly removes the cut shavings and cleanly re-cuts the threads.
As for the cover side, it's cosmetic only. If you're painting the covers, JB Weld or epoxy will fit it. If your power coating or polishing, then use a TIG and weld some fill back in, file and shape to smooth.