Each complete charge / discharge cycle (going down to 0% then back up to 100%) recalibrates the battery automatically. That said, it is not recommended to often let your battery go down to zero, and also not to keep the R6 plugged in at 100% while playing music at the same time (leaving it charging overnight is fine but if you're actively using it, I recommend that you unplug when you see it is fully charged).
The battery mode 1 and 2 apply different battery curves (and perhaps different 0% and 100% endpoints) to the device that correspond to two different batteries that the R6 have been supplied with during the production cycle. But I haven't been told how to identify that your R6's battery belongs to mode 1 or mode 2 or what the advantages are of setting the R6 to the right battery mode according to the actual battery inside. All I know is that both batteries have the same capacity.