atmega16u2 debugwire and usb device
Unfortunately no. Debug wire messes with the way a processor operates allowing the core to be stopped. While the core is stopped variables can be read out and written in. USB requires an always "on" type connection with stringent timing requirements. When the core stops so does the USB peripheral. That breaks both timing and always-on requirements. The host then rejects the device. 

I'm willing to bet if you run the processor in debug wire mode and no break points it would run just fine. Then when you hit pause the device would disconnect from USB. 

Debug using UART and capture the events using an FTDI cable.