I pretty much doubt that. If they did, you probably would not want to pay them, because not only the process takes a while itself, but they would also have to test everything afterwards to make sure it works properly, thus we could easily talk about a few hours here... (don't know the hour rate for an Apple technician).
Maybe the handles are still available and could be re-applied (even if it was an optical kludge) - probably less hassle than relocating every bit of hardware.
Oh and btw: You may want to run a hardware diagnostic - if the handles had to go in order to fit a desk, chances are that the little clearance left above the tower impaired heat dissipation, which could have been negative to component lifetime (even though it might not have shown up during your father's usual use).