Hey Kent,
The cyano has taken lots of phosphates out of your water / what it ws growing on (the sand?) and binded them up in cyanobacterial biomass. Siphoning it out will indirectly remove that phosphate from your system. Cyanobacteria, unlike all other algae, can actually take atmospheric nitrogen gas and convert it to ammonia if it is in a low nitrogen environment so cyanobacteria can even lead to nitrate problems if you have lots of cyanobacteria grow and then die. Do you test your phosphates?
HTH,
Kevin