Will this side affect be long term?

Ever since I started taking the pill a year ago, I have devolved stomach problems(digestion, going to the bathroom) Taking probiotics has helped me survive it but I was started to get fed up with it. After having sever stomach pain I stopped taking the pill however I still have these stomach issues. Do you think that my stomach is permanently damaged from the pills and my stomach will always be this way or that if I give my body time to adjust and heal it will go away?