Those are good points. Unfortunately at this moment I cannot refute or confirm with evidence, so my answer is largely speculative/anecdotal.

I would think it unlikely that large colon irrigation would cause significant change to the microflora of the system. A cursory pubmed search does not yield any data at all that would suggest it does (nor any that it doesn't). Again, a rinse out is unlikely to get rid of all the bacteria, as they can adhere quite well to the mucosa and, assuming you are healthy and eating as usual, then they would rapidly repopulate as they were barring other lifestyle changes (eg moving to a different country, doing this with a concomitant diarrheal illness, perhaps drastic diet change).

Weak intestinal walls is possible, as there would be repeated distention. What I cannot find or know is whether having persistently distended walls (would be the worst case scenario from repeated stretching) would have much effect, I guess a possible outcome of that would be slowed down system overall, which could lead to delayed time for stool passage, more water absorption, and constipation and risk of obstruction. Certainly possible but I cannot find anything online to confirm this. For instance, there is a disease of pseudo-obstruction called Ogilvie's Syndrome (which I have seen), which is intense distention, but I cannot really find, nor have I heard, of long term complications from this disease.

Rectal prolapse I would not expect. Usually that is a result of significant intra-adbominal pressure (as seen in persistent, severe constipation or, rarely, with heavy weight-lifters, etc). As I picture it, recurrent enemas, assuming a low flow on the IN and easy passage on the OUT, shouldn't cause any weakening of the musculature around the rectum leading to prolapse. For this reason, I also wouldn't expect things like hemorrhoids or anal fissures.