I need to use Segger J-Link with CYQ954907AEVAL1F, but I am quite concerned, because there looks to be a short-circuit between the JTAG header and the FT2232HQ. The FT2232HQ seems to be configured using a EEPROM (AT93C46D). This means as soon as power is applied top the board, the FT2232HQ will activate the FTDI_JTAG_TCK, FTDI_JTAG_TDI, and FTDI_JTAG_TMS pins as outputs.
If I connect a Segger J-Link, then there will be a short-circuit between the Segger J-Link and the FT2232HQ on pins FTDI_JTAG_TCK, FTDI_JTAG_TDI, and FTDI_JTAG_TMS, as both the FT2232HQ and the J-Link will continously drive these pins as outputs.
This issue has been reported before, but was never properly understood or answered:
Your understanding is correct in this regard. The recommendation is to use the external power jack (J8) to avoid the short circuit. Unfortunately, this is a shortcoming in this kit design and I have passed it along. But if you use the external JTAG debugger like J-Link, Olimex connector, would recommend you to switch to the power jack for providing supply to the kit.