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XDS100v2 CPLD programming

I have a board with that includes an XDS100v2. The XDS100 portion was designed following the refference design except that it has the recommended changes to support using port B of the FTDI chip as a uart. I've tried the utility listed on the wiki but since the connections were changed to allow for use of the uart the utility will not program the CPLD.

Is there a way I can program the CPLD over the USB/FTDI connection?