I do not know the product you have been using, but Colo Zone or Colosan are not known for causing any side effects.
Probiotics may be useful after the system has been cleaned out, but then it may not even be necessary anymore. It is much more preferable to stimulate the body's own production of friendly bacteria (they breed in the appendix and are then mixed with the incoming intestinal waste) than supplying them externally (which may make you dependent on them). However, if your appendix is out, then taking probiotics may be a good solution.