I can’t see why probiotics would affect the antibiotic treatment. They won’t support pathogens like the one in your tooth, and if anything will compete with them. Antibiotics will just kill whatever bacteria they come into contact with. You’ve just gotta hope they don’t wipe out any entire beneficial species. Probiotics act as support but not replacement. They should help keep candida under control while your indigenous bacteria are weakened by the treatment.
After this is over, I’d take a look at your dental hygiene regime. Make sure you lightly brush all the gum your brush can reach twice a day. You don’t want to give bacteria a chance to grow anywhere in your mouth. Using a decent mouthwash should be useful. Flossing more frequently and avoiding any source of starch (buckwheat, oat bran etc) for a while might help too. Vitamin D and K2 are vital for good dental health, so start supplementing them if you aren’t already. See this post about healing dental caries for an example of what the right vitamins can do.