Someone here (MMsTSX ?) bought an SC but got a wrong reflash by mistake. They gave him the reflash for bolt-ons instead of SC. The car gained power and didn't break in like a year of driving. It did not blow up or anything but only when it was dyno's and VTEC engagement point at 5000 rpms was revealed was it clear that there was wrong programming of the ECU. I think it gained like 10 HP after correct reflash was done.
So in conclusion, your reflash CAN work with SC, its just that u do not want it to.... Oh and if u are reflashed, there is a $100 discount for SC. I would rather exchange your ECU for a non--reflashed ECU + $300? $500? Then I would program that "new" ECU to work with SC
