I don't think it'd be "healthy" to discharge a pack with mis-matched modules that have a different cap, which is why most EVs do balancing from time to time. As I understand it, the BMS can do balancing per-module. From what I've read on the subject, there is a circuitboard that can at least report the minimum and maximum cell voltage in each module but cells can't be balanced individually.
More speculation on my part but I figure, we don't have anything but speculation at this point so... it's my guess that after the update, the BMS looks at the min and max individual cell voltage in each module and if it finds a module that has a high enough delta (difference between the lowest and highest reported cell voltage in that module), it labels the module as having at least one cell that is "out of spec" and caps you. If there are 444 cells per module and you try to charge that module to spec voltage for the whole module and there are some individual cells in that module that have reduced capacity, you'll end up with some cells overcharged to reach that overall module voltage. It may be that they reduced the max charge voltage to avoid this, thus "limping" the entire pack to the weakest link (module).
Mike
Nice write up. That pretty much sums it up.