I used to be afraid of the same thing, I read somewhere (probably some mainstream doctors wrote it) that if you do colonics you can flush out the good flora and that it can actually harm you because of that. Nothing could be further from the truth. One of the first things I did way before I tried colonics was to consume large quantities of good quality probiotics (I took Primal Defense - around 8 a day for months) and hoped that alone would help and improve my condition. I thought the good bacteria would take over and my skin issue would be solved (I intuitively knew my colon had something to do with it, but didn't think I needed colonics at the time). Well, that alone didn't work at all. It is probably too much of a job for those good critters to eliminate all that stuff accumulated in there. So don't worry about that, you probably have more bad bacteria than good anyway, and once you're clean it's easy to plant the good one there. Start taking probiotics after your first cleanse and keep taking it. I still take Primal Defense for maintanance. Also, another benefit is that my bowel movements have improved after colonics, they're easier and bulkier.
Good luck, and report you progress.