Ah, OK. Never heard it called stacking before. Crashing, wiping out, taking a tumble, taking a dive, a spill, even plain ol' falling I'd understood right off.

Then it's not your responsibility. A properly engineered drive line shouldn't fail like that. There should be a fuse (or some other limiter) that'd blow before the motor/gearbox is allowed to torque itself to death.

You've gotta look at the whole assembly, vehicle + driver. Sure, the new batteries are a lot chunkier than what you had before, but what was that in proportion to the overall weight? I'm guessing maybe a 10% increase total. It'd have to have been a fairly borderline system to start with if 10% was enough to break it.

A proper bike trailer, or something improvised that clunks around a lot? If the motor is shoddily engineered, reverse torque may be an issue. A very sudden increase in load can certainly contribute too.

The speed would be greatly reduced. Electricity is often compared with water. Think of the batteries as a tank. The volume of the tank is similar to the capacity in amp hours, and the voltage is similar to how high the tank is sitting as compared to where you are.
Say that at the moment you have the tank 36 feet up in the air, and a hose running down to ground level. Open the hose and you get a decent squirt out of it.
If you decide to go with one battery, it'd be like only having the tank 12 feet up in the air. Opening the hose now would give a much weaker jet of water. And it's the strength of that jet of water that's pushing you forward.
You might get away with using 2 batteries though, but it depends on how clever the control electronics (the throttle) are. If its' built only to accomodate 36 V systems and you start feeding it 24 V it might decide that something is seriously wrong and shut down immediately.