Typically with any controller / display set that come in different voltage sets (rather than autoadapting, or having a menu or switch to select this), the battery meter and the LVC are set for one or the other; there's about a 4v difference between the two types (one cell's worth). Some also have an HVC that prevents operation above what it expects to see at full charge.
If you have a 52v unit and a 48v battery, it will shutdown well before the battery is actually low, so it will not let you get the full range from it. The battery meter will never show full, either.
If you have a 48v unit and a 52v battery, it wont' shutdown on it's own as the battery empties; the battery's BMS will probably have to do this for you, which is hard on the battery. The battery meter will also probably show full or near full for quite a lot of the actual battery capacity, though it really isn't. If it also has an HVC, it may not operate when the battery is fully charged--you might have to use an adjustable-voltage charger and charge it only to 54v instead of the full 58, in this case.
Regarding the BBSHD specifically:
There may be firmware updates you can do (some threads around here for them), but I wouldn't count on them--they may alter other operation you dont' want to change, or they may not work, or worse the controller could be bricked trying to do the update.
I think there is also a thread here to do a hardware mod for this voltage issue, but, again, it's possible to damage things with modifications.