You bought an expensive bike, with complex, custom, PROPRIETARY wiring and communication between the battery and controller. Only Bosch has specs and equipment and knowledge to fix this problem. You should have the same range as the first, new, battery provided, what the system is guessing is not relevant. I would say to do a total wipe and factory reset on the electronics, but this should only be done at a verified Bosch dealer with a written guarantee that a replacement bike will be available if the procedure results in your bike no longer working, AND such replacement bike is on hand and immediately available. Because such a result has happened before in similar situations.
Also, I do not think they are "stumped", rather that the system tracks battery state very closely to make the estimate, and they made no provision for more than one battery being available. If you do the reset as stated above, I would bet money that your original battery will no longer show the same estimated range. The Bosch people just do not want to admit this really silly error. Go to your dealer and ask them if these results would in fact occur if you do the reset. Look in the menus for any sort of Battery #1 or #2 selection, or any ID codes for your individual battery, bet there ain't any.
My replacement battery was inexpensive, and connected easily with red and black power wires ONLY, I do not need an expensive computer with no knowledge whatsoever of environmental and road conditions to make a GUESS at my projected range, I know from my state of charge, wind, weather, and hills on my route, and how much effort I feel like putting out, what my range will be pretty closely. Note that your bike knows ONLY the first of those data.