If the 6 volt battery is still connected - in theory it will load down the 12 volt battery and help to regulate the voltage to 6 volt system for a short time.
Be very careful when connecting a 12 volt battery to a 6 volt battery of unknown charge state. A large current will flow to the 6 volt battery resulting in gassing of both batteries. Any spark can ignite these gasses causing an explosion. This is true even when a 12 volt to 12 volt connection is made.