My two cents
I suspect that you have damaged the hardware in some way but from your description I'm not sure which part; I'm not talking about the scratches on the crystal.
If it's not recognised, the problem relates to the 16U2 USB-to-TTL chip (near the usb connector) or circuitry around it (e.g power). So updating the boot loader will not help.
Updating FTDI drivers will not help as the USB-to-TTL chip is an Atmel and not a FTDI.
I would not try to fix it. There might be more damage than you originally found and that can result in an unreliable Uno which will give you gray hairs during debugging or at run-time.