I had issues with using flats with dual narrowband, where the same flat gets applied to both Ha and OIII. To overcome this I developed a script to extract the Ha and OIII from the flats and calibrate the Ha lights with Ha flats and OIII lights with OIII flats.
Not sure if anyone else wants a copy
Regards Paul
Why don’t you apply master flat directly on the CFA image (Ha+Oiii). As it should be.