I did experience a lot of discomfort the first 5 days which is why I think you should start the program on the weekend. I don't think it will affect the medications you are on but since I'm not a doctor, it may be best for you to call your doctor and let them know what you're about undergo (colonix).
That being said, the discomfort is really a detox process so if you're aware that what you're feeling is happening so that you can feel better, I think you'll be encouraged to keep at it. I've been off Colonix for 2 months now and I'm regular like a clock. When each new year comes in, I'll order a one month supply but other than that I won't take it again.--good luck, I hope this helps you!