I don’t think that actually answers the question though… do you know if the CLR is running on the device at that time, and it’s just the USB that isn’t working? Can you deploy a “blink LED” app on the device when in your HDR carrier, and then check if that’s running when you have it installed ?
Have you taken a good look at the board for solder issues or reversed components? Given it’s a custom board, perhaps you have a design issue? Is it worth posting your schematics ?
I think that it’s going to be hard to get further as-is, because your module works outside the board --> that to me implies that your board is definitely at fault which is why that’s where the focus needs to be.