It is not killing probiotic cultures in your bowels.
And 6 weeks is not really longterm, especially since
fluconazole is not an antibiotic, but an antifungal. Candida is a mean one, and hard to get rid of. But Candida hates a balanced diet with lots of beans, veggies, wholemeal, yoghurt and fruits. Reduce your meat and sugar intake to aid the meds to kill it off. Good luck!