[Mr_X]

you will not remove your beneficial bacteria with waterchanges. all you will remove is excess nutrients. you'll need to get rid of all the nutrients you have been adding and not removing thus far. it's going to take a while.
the cyano will not be gone over night.
shutting off the lights won't stop it either.
siphon out as much cyano as you can with each waterchange, increase the flow in the areas where you see it originating from, and that's about it, besides chemical means. the chemical available for this issue is erythromycin, an antibiotic.
it's questionable whether this will effect the good bacteria, while killing the cyano. some say it will, some say it won't. i feel that antibiotics have no place in a reef tank.
besides, you are only removing the byproduct of the real problem which is excessive nutrients.
IME.