Would have to think about it more, but I believe the current setup would work (as it creates the readGroup Id mapping on the fly from given ADAM records) but the new change would not since it fixes a mapping based on whats in the header and different ADAM records could have overlapping ids from different read groups.

But my question is, right now this is being used in BQSR to optimize the way we store counts per read group.  Is BQSR a well defined operation across multiple BAMs/ADAM directories?