Troubling to hear about your fish losses, Keith.
Koi are bottom feeders, so I wouldn't be surprised if some of that construction debris caused them some problems.
I smiled when I read of your wife's wishes to move the pond over a few feet...it reminded me of my wife when I built her dental office and she wanted a wall moved a foot or so. No problem, it's just a bearing wall that included mechanicals. I did as she asked, and as usual, it was worth it. Not a small task though.
When moving your pond my only advice is to make sure you have a mature filter ready to handle the fish waste in the temporary holding tank while you move the pond. Cleaning the liner and starting over is probably a good thing considering the possible contents of the debris sitting on the bottom.
Good luck!