Not an ideal set up.
However, placing a 100 ohm resistor or similar from each battery + to the MPPT B+ terminal should give it enough current to sense the battery voltage, while maintaining some degree of isolation. Better solution would be to connect the MPPT directly to one (the better) of the two battery banks and use an ACR relay (Cyrix) to charge the second battery. The relay will then isolate the two banks during the night.
I will try the resistor method tomorrow and see what happens.
I do have a kilovac connected to each bank so I can switch them over when I want. So your idea of a voltage controlled relay may be easy to implement to switch the kilovacs.
Thankyou for your response, it has given me some good ideas to try.
Hi Mike I tried the 100 ohm resistor workaround this morning. That did not work on my system, so I tried a 60 ohm resistor from the B+ to the MPPT B+ terminal and that worked great.
Thankyou once again for your help.
I am guessing that there will a small leakage current during the night from one battery bank to the other but at the moment the system is working and charging both battery banks which is what I want to do.