Okay, so I had an STK500 driver connected on USB on virtual COM3. However, after installing and uninstalling some software, the drivers futz'd up, and ceased to detect the programmer.
So, I've reinstalled STK500 drivers, and set device to use COM4, as COM3 appeared to be in use and couldn't be re-selected.
Now, Atmel studio 6, under tools / Device Programming, there's STK500 on both COM3 and COM4. It's annoying, as for some reason my project tries to use COM3 instead of COM4 when clicking 'Debug'.
How can I delete the COM3 device from there? I can add devices under Tools / Add target, but I can't find anything like 'Delete target' anywhere.