Like Christian, I use the keywords feature of WBPP associate different calibration masters with different groups is lights, letting me process everything in one go of WPBB. I use the keyword feature for other attributes than which flats go with which batch of lights. I've added add to projects in subsequent years, and the new data needs different darks as well, so I can use a darks keyword to associate with different groups of lights. I even switched the sensor temp at some point, so I used a temp keyword to associate lights taken at one temp with lights at another. Keywords can be used for stuff unrelated to calibration frames. When I shoot a mosaic, I group my panels with a panel keyword on both the pre and post phases of processing, so WBPP won't try and integrate the subs from all the panels into a single image.
I also recommend the Adam Block videos. He has a whole series on WBPP, but I believe this is the one discussing using WBPP keywords.
https://www.youtube.com/watch?v=J6tif1v8hmY