You can stay on the nefedipine as long as you like, it is just a BP med that's been compounded into a cream, and as you know, many people take BP meds for their entire lives. I wouldn't worry about changing to diltiazem, as they are both very equivalent.
When I had an active fissure, I noticed a huge decline when I stopped using my nefedipine. So stay on it until you have been diagnosed as 100% healed.
Also, try to regulate a high fiber diet to ease your mind about diarrhea. If you try to eat pretty much the same things every day you will probably get a more consistent stool, but that can be a very difficult thing to achieve.