I used some firmware I found online to turn the UNO into an emulated HID device. The Arduino is no longer connected to a Serial COM port so I can't send serial data from my computer to the device. Is there a way that the Arduino can receive data from the computer in order to drive a function while in the HID emulated state?
You could use a second USB on the PC and use Hardware Serial to transmit commands. (Either via a second Arduino or a FTDI adapter)
But be aware that at least the firmware I use and the controller programs are very sensitive to being disturbed in the loop. So you should have a good understanding of timers, interupts and non blocking code.