Welcome to the forum. Thanks for your question.
Internal rectal warts are a difficult management problem. There has not been very much systematic research; most of what we know is based on the reported experience of protologists and other who treat them. In general, they appear to clear up within a few months, sometimes longer -- but until then, recurrences are not uncommon. Part of the problem is that even the best experts, using anoscopy or sigmoidoscopy, cannot easily identify all internal warts -- so that what seems to be a recurrence is often just a larger wart that was missed on the previous cycle of examination and treatment.
Most of the time, there probably is no serious harm in watchful waiting, rather than repeated episodes of surgery. However, some cases will progress to a point at which the surgery becomes more major than otherwise necessary. If you are under the care of a proctologist or other expert, I would ask him or her the same question
For external (anal) warts -- and for external genital warts, for that matter -- the individual responses vary widely to the various treatments. Some respond well to freezing with liquid nitrogen, others better to podofilox (Condylox) or imiquimod (Aldara), still others to trichloroacetic acid (TCA). If the response isn't great to any partiuclar treatment, the usual approach is to try one of the others.
I know it's a frustrating problem, and I'm sorry there aren't easy answers. But the long term prognosis is very good; you can expect the problem to eventually resolve and stop causing problems.
Best wishes-- HHH, MD