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TMDSPREX28335: Using Peripheral Explorer Kit with an External XDS200 EMU, Can I Use the On-Board USB for Comms to a PC without the on-board EMU interfering?

Part Number: TMDSPREX28335

I have the Peripheral Explorer Kit using a 28335 Control Card and an External XDS200 emulator. The schematic shows that the on-board USB has two output ports from the FT2232D IC on a USB section called M1, one for the on-board xds100 emulator functions which I will not be using, and the other seems to be a connected to a SCI serial communications interface on the 28335 (GPIO pins 28 & 29). As shipped, there is an open jumper on the Rx side of the Peripheral Explorer board (J4) blocking any received Rx from CH:B of the FT2232D IC going to the 28335. If I were to short that jumper, are any other changes needed to keep the FT2232D CH:A signals used by the on-board emulator from interfering with serial communications from the 28335 thru the USB to a PC?

Also, where can I find additional information on how to switch the FT2232D chip from using CH:A to using CH:B, or are they both active simultaneously? Perhaps there's some additional documentation on this TMDSPREX28335 board (using the 28335 control card) that would get into more detail on how serial communications are done, including details on the on-board xds100 emulator?