I may be wrong on this but here goes.
Using Erythromycin will likely not do much to the good bacteria in the tank. Most *MOST* beneficial bacteria is gram negative, Erythromycin is good at killing gram positive bacteria. So the cyano gets it cause it's gram positive while the filter doesn't really notice anything cause it's gram negative.
If you have alot of cyano and you nuke it, you just have to keep up with lots of water changes so the dead and decaying yuck doesn't mess further with your parameters.