Covid question and root canal antibiotic

I have severe jaw and neck pain.And one tooth#46 which hurts for 2 years for tapping and biting pressure on it. But nothing seen on the CBCT scans and xrays. Had root cash in 2020& no relief.Had partial retreatment in distal root last year and no relief. I decided to remove the tooth since it's hurting constantly but nothing found on it. But the Endo wanted to do another retreatment before pulling that tooth.So he opened whole tooth on Tuesday. He said he saw the fillings so wet in mesial canal. He said it's stinks and blood color like purplish. He didn't see any pus.Didn't tell me if it's infected. Put me on penicillin VK for 4 times a day for ten days. Placed medicine inside the canals.I don't know if these signs indicate infection?Do I need to remove the tooth immediately? I'm worried if the infection will spread. my kid(8+) tested positive for covid yesterday. I tested mine and was negative.I don't know if I can keep taking antibiotics for ten days even if I get +ve in few days?