As long as you take the probiotics at least 2 hours apart from the Antibiotics you should be fine. Upping the dosage would be a good idea but don't go crazy.
Can a dentist prescribe Nystatin?
You'd be best off getting an expert opinion regarding Antibiotics and a perscription antifungal at the same time.
I was in a similar situation and went through 2 courses. It may be a minor set back but its better than the alternative - dental pain.