Some meds do harm the beneficial bacteria. I don't know what you used, and even if I did I couldn't tell you if it hurts the cycle or not. That being said, if this is part of the trouble, then the pleco could be more stressed out because it was already ill to begin with. With healthy fish a small cycle normally won't bother them much, but sick fish or fish that have recently been sick are more susceptible to stress and the effects.