This may be a silly question, but have your periods returned? The sudden onset of pain while pumping like this reminds me of the month my cycle returned, because I also had this out of nowhere sensitivity to turning the pump's suction up to where I usually kept it. For some reason, pumping really, really hurts me when I'm ovulating. My nipples are crazy sensitive for two days, mid cycle. Nursing, strangely, does not hurt me during this time, but pumping is insanely painful for me!
I also did have to increase my flange size after about two months of back-to-work pumping. But it doesn't sound like the pain you are experiencing is constant, or due to rubbing or poor fit--which is why I asked the longshot question about your cycles!