I’ve never seen anyone put forward a possible reason on why these boards lost their bootloader, but in terming of fixing the problem, people have been successful. Here is one topic on the issue. You need a USB to TTL module to burn a new bootloader to your board. It can also be done with an Arduino if you happen to have one of those around. Once you have the new bootloader installed, you can then flash the V1 firmware.
You may want to do some troubleshooting of your current SKR Pro board to determine if burning a new bootloader makes sense. It was just one idea I had that might resurrect your board.