After my own experience with Chlamydia not wanting to go away, I would definitely recommend going back for follow up testing. Medically speaking, a doctor will usually advise you to come back in 3 months. Have your chlamydia symptoms came back, not including the bowel issues? That has been an issue for me somewhat for the chlamydia symptoms to "subside" and then all of sudden start perking back up. If you're only experiencing the bowel issues, then I wouldn't be too sure that Chlamydia was the issue. It's possible to get infected in that area with Chlamydia, but I have not experienced that personally. Since you still have concerns following your treatment, I would try to get back in with a doctor as soon as you can.