Hot alternator

Sounds like you are taking good care of things. If the battery failed with a cell short, the current could go high because a 10V battery can not reach the desired voltage. The regulator and alternator tries. Typically a battery short is not very low impedance, but it can be.

Large motor loads carry high current, and are inductive. When switched off, the current still wants to flow and the voltage spikes. That is seen as a reverse voltage to the diodes, if high enough they can be damaged. A way to prevent at shunt the motor with a suitable diode that is reversed biased, it will circulate the current and eliminate the spike. It is often called a freewheel diode. A good battery serves to stabilize voltage , like a huge capacitor, and actually protects the system.

If the battery has an open cell, and is running all sorts of damage can occur, especially with electronic devices. This is because regulation will be all over the place as the battery cuts in and out. Operating the battery cutoff with a running car takes careful design and considerations.

If you have a schematic for that, we can look and see if perhaps the problem is related.