I have a VMF copygun that preserves constraints. No thrusters, and any other VMFs that are part of it get borked, but it preserves constraints. I tested it by taking a jeep, slapping headlights on it, welding a thing to the top, a door to that, and dragging a vending machine door behind it roped to the door.
When I copied it, it was exactly the same. Except a headlight keeps falling off for some reason. But hey, one out of all of them ain't bad.
I can find a link/reupload, if you want. It also comes with an LUA interface for loading patterns, and a handy menu to spawn VMF SWEPs, turn Ghost Preview on/off, set exact rotations, etc.
If you REALLY want to make a VMF save, have Hammer running in the background and use the "export to hammer" function, then save as VMF. That *should* preserve everything, including scripts. Maybe. Never actually used it, so I don't know.