Hi Pablo and
to the forum.
I have not had any direct experience with the VEC-300 controllers so I don't know whether the 72v Controller will work on a 48V battery, but if the 48V option is available in the program setting software, I would suggest that you simply try it out and see if it works, as you shouldn't be able to damage the controller with a lower than expected voltage.
I don't know if the VEC-300 controller needs to be powered up like the vector controllers in the hub motors, but if it does, I would expect a 48V battery to have sufficient voltage for this purpose.
(The vector hub motor controllers can run on 24V, 36V or 48V batteries, but I have used a single 12V battery as a power source just for programming purposes.)I don't know if the e-lock function will affect the controller programming mode, but you should be able to easily bridge it if required.
Alan