Yes you can sub peppers for peppers as long as the total measured amounts are kept the same.

Flavor is bound to be altered since banana peppers have more heat in them than bells. Whether that flavor change is acceptable only you can decide. Scoville rating for bells is zero but the rating for banana peppers ranges from 100-900.

Dave

If it is sweet banana peppers, I don't think it would make any real difference. Obviously hot banana peppers would up the heat content significantly.

Thanks - I plan to use sweet bananas. I may try a batch with just a few hot bananas but then use mild jalapenos. Will see how it goes!