You don't have to disconnect your batteries to charge, simply move the 36v charger wire back to 36v (the 6th battery), then just put the 6v charger on the 7th battery.
The 1206 is an Ezgo OEM controller and I don't think the 1206 Curtis is capable of 42v unless they upgraded the voltage as well when it was rebuilt. You will have to confirm this with the company that did the modification.
If a controller is supplied with too much voltage it will not work, it goes into an over-voltage protection mode and shuts down.
To confirm this, connect it back up to 36v and see if it works.