Can I use Arduino's FTDI chip for another device?
We don't know if ATmega16U2 is damaged or not but assuming it isn't you can use it as a generic USB&lt;-&gt;USB.
According to this FAQ

The Uno has changed that by exchanging the FT232RL chip with an atmega8u2 chip. There are a few things that are possible with this new chip but before we discuss that lets make it clear that by default, this chip acts identically to the FTDI chip that it replaces. It's just a USB-serial port!
One improvement in updating the chip is that, previously, Mac users needed to install FTDI drivers. The 8u2 imitates a 'generic' CDC serial device. So now, Mac users do not have to install a driver. Windows users still need to install the .INF file but luckily there are no drivers. This means there will be fewer problems with new versions of windows. There is no way to have a serial USB device that doesn't require an INF file in windows

So is will be enumerated as a virtual serial port, you just need to locate the port number in the hardware panel of the PC.
Also note that the Rx/Tx are connected to two pins of the header but at the same time are connected to the damaged MCU so maybe that will be a problem altough I doubt it.
(red/blue are the Rx/Tx lines)