I am just trying WBPP for the first time. I have a rotator and have to match E/W flats with E/W light frames, so following Juan's advice from an earlier post I defined new custom Filter groups for each combination, e.g. Red_East for the lights and flats.
I also unchecked Apply in the Integration box to prevent WBPP from integrating East and West separately.
But trying to Run, I immediately had a problem (I expect the same with the old BPP): for one of my filters I only had 2 East light frames so I got an error (Cannot integrate less than 3 Light frames) - even though I had unchecked Apply Integration. So there is no need for this error when integration is not required.
But the main point is, does this nullify the advantage of WBPP, because the Weighting Presets are only applied during integration? In other words, up to the Register stage is WBPP the same as BPP? If that is the case, I can't see any advantage in using WBPP with E/W flats.
The only solution I can see would be to enhance Image Calibration to read the FITS keyword PIERSIDE and match the Lights to the corresponding Flats. Then there would be no need for these extra filter groups which prevent WBPP running Image Integration.