Ref. schematic R4006-G0001-03-SC-REV02.pdf
If using the USB interface (FT432, sht. 24), the FPGA JTAG signals are double-terminated by resistors shown at sht. 24, zone B11:

and sht. 10, zone J4.

by way of the mux'ing shown on sht. 24 "JTAG/SPI_MASTER_SEL".