I've tried with my external FT232H and UPduino v1 to elaborate how to use the Serial UART over USB in the same wiring as it is with the new UPduino v2.
Experimental, use at your own risk.
It works, when:
1. insert 3x 680ohm resistors in series with FT232H's pins 13 (TXD), 15 (RTS), 17 (DTR)
2. you have to redirect your fpga app's RxD/TxD to UP5k's pins 14 (TxD) and 15 (RxD) such they will be active only when UP5k's pin 16 is high (pin 16 is connected to the chipselect of the bitstream flash), the UP5k's pin 15 is an "inout" based on the 16, when 16 is low you may use those pins for the flash SPI access when applicable (ie. I've been using the flash SPI with the above mentioned
Forth for load/save the dictionaries from/into the flash).
Mind when writing the SPI flash while in console you will see a garbage coming in..
3. you have to reinsert the USB plug as the Diamond programmer leaves the FT232H in SPI mode (the FT232H starts in Serial UART mode when you open the COMx in your terminal app, ie. in TeraTerm)
4. you have to toggle the DTR to 'High' within your terminal app, otherwise the UP5k will not boot from the bitstream flash (the UP5k does sense the SPI flash chipselect (wired to the DTR) and when high it boots from the SPI flash).