I have two battery banks, and I've done something like what you are describing, but for a different reason. I have a total of four 6volt batteries wired in pairs in series to get two 12 volt banks. The charge controller is attached to the minus terminal of battery 1 and the plus terminal of battery 4. The minus terminal of 1 is also connected to the minus terminal of 3, while the plus terminals of 2 and 4 are connected to each other.
The minus to plus connection between batteries 1 and 2, and also 3, and 4 are attached with wingnuts. Periodly whenever I want to equilize one bank or the other, I unscrew one wingnut between 1 and 2, or 3 and 4 (but never both). That way, 100% of the
solar power can be directed at one bank at a time untill that bank is 100% charged (as indicated on the charge controller). In this way, one bank or the other won't pull down the efficiency of the other bank.
Hope that was informative.