Well, your first mistake was putting hives several hours away. Regular care of the hive prevents a host of problems. Thats why it's called beeKEEPING. ;) If you put your location with your avatar, we can give advice tailored for your region. For example, if you're in Australia, we can rule out varroa infestation. I can't say if it was SHBs since I don't know where you are. They haven't gotten to a lot of places up north. If you have them in your area, I'd say that's the culprit. It takes constant vigilance to keep them in check. Even with regularly working my hives, I lost SEVEN hives to them before I found the way to control them. Did you see piles of dead bees? They may have been poisoned, but this far after the fact, the heaps of dead bees may have disappeared. Was there dead brood in capped cells? If they weren't queen-right, they may have just died off. I've seen queenless hives diminish to the point that there aren't enough bees to maintain the right temperature on the brood so they start to die in the cells.
You asked about reusing the foundation? Did you mean comb? If the bees were there for any length of time, they should have drawn out the foundation (unless you put on way more hive than they could fill). Old comb becomes dark and travel-stained. Either way, I'd clean them up and reuse them. Even if the comb is funky, but not too full of holes, they'll clean it up and repair it. Otherwise, re-foundation the frames. If the moth holes are over an inch or so, they may repair it into drone comb, which you may not want. The only reason for destroying the equipment is if you had foul-brood. Some states require it by law to stop its spread. Thankfully, it is rather rare. Given how long the hive was neglected, it it hard to say why they absconded or died out. If it was varroa, they die without bees around, so no worry about them contaminating the frames. I'm not sure if trachael mites can survive in the absence of bees, but I don't think so. I think wax moth and SHB eggs remain viable for awhile so I usually freeze my frames to kill off any residual pests.