I am now running the 36V controller at 48 volts (4x12V SLA). I'm not sure how long it will last, but it is working for now. The only change I had to make was to add a zener diode in line with the large 150 ohm resistor feeding the 15v voltage regulator (one of two TO220 ICs on the controller board). The zener must be enough to drop the voltage at the input of the regulator to around 48v or less. I used two 4.3v 5W zeners connected in series. That way the voltage is still OK when running at 36v or 48v. A single zener of 5-10 volts and a 5W power rating should be fine.
If you want to have a correct low voltage cutoff for 48V, add a 3.5k or 4k resistor into the location marked R4 on the board (it normally has a small wire instead of a resistor.
Personally, I just added the zener and left the low voltage cutoff alone. That means that I can use the 36V battery the same as always, and when I'm running the 48V battery I just have to be careful not to over discharge it.
If you need more info, just ask. I'll post again in a few days to let you know if it is still working.
Pete