I’ve replaced the ECM but not the prom. I’m not driving with the OBD jumpered.the only thing that should make the engine light flash while driving is if it is in field service mode if ALDL terminal B is grounded (either jumpered to A, or perhaps a wiring issue). the flash speed varies based on open or closed loop. but it should not affect drivability, I don't believe.
but I've also read accounts of a bad ECM or PROM or Calpak, etc causing a flashing light while driving.
if the light comes on solid and later goes out, the code should be stored for 50 starts or power removed from the ECM for 30sec. so something strange is going on that no codes are stored.