May be you should have different mapping file for each region, and then carry out further analysis? For that one should have proper sync with lab-technician to provide samples which fall under which region.

Also, my understanding is, a particular parameter might not work all the same with different region. E.g.: Quality for V4 might not be applicable for V3-V4 region, and, or vice-versa.

Does that mean the pipeline has to be run end-to-end for each region separately?

I'd love to hear some solution here. I've recently stumbled onto this: multiple regions sequenced in one gigantic raw file. Thanks.