Assuming nothing has exploded but the 12 volt battery eventually dropped in voltage to a point where the device cut off the supply you are left with a fairly flat 12 volt battery and a very flat 6 volt battery. Charge all the batteries at the same time.

12 24 Volt Dc 1500 Amp Series Parallel Solenoid Relay
Charging 12v batteries in series. Thats the pat answer. 147v total and then float around 135v. Charge more than five batteries by connecting one 12 volt battery charger across each battery in the series as if each battery were the only one being charged. This means you have a fully charged 48v battery pack with each battery at the same state of charge. Charging only some of the batteries will result in batteries attempting to equal out the power and charging each other. Then connect the negative end of the battery to the positive end of the next one and continue to do so for the rest of your batteries.
For the final battery connect the negative end of the battery to the negative output in black of the charger. Two 12 volt batteries wired in series produce 24 volts but the capacity remains the same as one for a 12 volt battery. You need to overcome the total voltage of the series batteries 12 v 12 v 24 v to drive electrons. Two 12 volt batteries wired in parallel continue to produce 12 volts but the capacity doubles. Batteries may be wired in parallel or in series. As the batteries charge their voltages rise again and this time the smaller battery charges faster.
Charging 12 volt batteries wired in parallel requires a 12 volt battery charger. After your 4 12v batteries are all topped off take them out of parallel and wire them in series. One basic configuration for charging batteries in series is to connect the positive charger output in red to the positive end of one of the batteries. To charge two 12 volt batteries in series youd need a 24 volt charger. Note that a 12v battery will charge to approx. Make sure that your 12v charger is rated for the type of batteries youre using like sealed vs.