In Mutants&Masterminds it mentions that if your mecha is destroyed then they can no longer be repaired and they must be rebuilt from scratch. Does that mean that the points you invested in your mecha are simply gone if your mecha gets destroyed in combat or do you simply need to redesign your mecha and rebuild it from scratch with no point cost involved?
Just like any Device or Equipment, you eventually get the item back, or get to spend the points somewhere else, but it may not be immediate and/or it may require skill checks or some sort of quest for parts. Of course, if the mecha was found gear, or a gift, it might be gone forever. The system does not really support accruing loot.
Specifically, under the Volatile Drawback, they note:
A destroyed mecha can be repaired (see Mecha Repair, near the end of this chapter), or you will get a replacement after the encounter (or a couple of days).
And from Mecha Repair:
A destroyed mecha (as per the Volatile drawback) can become Dying with two weeks of constant reconstruction.
Mecha are vehicles, purchased with equipment points. Equipment points come from the Equipment Advantage.
The Equipment Advantage is a part of the character, paid for with character points. Therefore, the character does not lose the ranks of Equipment.
However, equipment is mundane stuff, that can be broken or taken away. It can also take time, special resources, or even adventures to replace rare and complex equipment. If replacements aren't available, as determined by the GM, then the equipment may be lost forever, but the equipment points are retained and can be used to get completely different equipment.