As the camera did not rotate with respect to the telescope, then one set of flats will work both before and after the flip. But, are you taking flats on each night? this is so imporant for the flats to work properly as conditions change from night to night, different focusing, dust on the sensor, sensor window, filters etc can move. If your using filters, you need a set of flats from each filter.
This means you need to calibrate each set of nights subs seperately and then during integration all the subs from all the nights are integrated together.
Mike