I see, you have a primary battery and solar array, plus a backup battery with 3 solar panels on it just to maintain it. So you need to be able to switch the charging sources when the backup battery is in use.
I still think that switching the solar arrays from one controller to the other would be the best option. It's a simple matter of swapping four wires (the inputs to both controllers) from one to the other. I would imagine the panels are typical grid-tie panels with three in series, running at about 90-95V under load, around 120V open circuit, which would be the same as we have, except we have 40 of them on four MPPT 60's (250W panels). I wonder if Midnite Solar might make some DC switches rated for the appropriate voltage that you could use to make a switching system for the high voltage part? By simply swapping the arrays, the controllers are never disconnected from the low voltage (battery) DC power, so it should not harm the controllers in any way.
I think it would require four two-pole switches to make a switching system.