1) lets be correct you are talking about Future Creative board with Microsemi FPGA :)
the problem you describe is real and there is no workaround possible, you do have to disable and re-enable FTDI D2XX support (required for Libero) to be able to talk the virtual serial port.
This makes it virtually impossible to use Linux host for development, it is so annoying that I would immediately go to saturn/walmart and buy extra winPC to avoid this headache. The price of that dev-winpc would be worth my time in frustration.
I can not say what is the root cause for this, the developers of Quartus support for FTDI based JTAG adapters say that this is because of problems with Linux drivers and a workaround is not at all possible (because of major issue withing linux driver system).
I know the linux folks say that there is no issue related to Linux/drivers.
Be it so or so, at the moment there is a co-existance problem between D2XX drivers and VCP (virtual serial port) on Linux.
On Windows such problems do not exist, Philosophers UART messages just stop during the programming by Libero and restart when its done.
When I first heard that this basic and simple functionality is not at all possible on Linux system because of issue with linux driver system I was almost not believe this claim.
Sorry Tommy,
I can not fix linux drivers D2XX issues for you, and also not for the judges, they will go crazy if they really want to re-flash and verify UART on same linux host.
OTOH - Lattice and Gowin USB JTAG adapters do not include the "load D2XX" bit in the EEPROM, and those load VCP for all channels, maybe here is theretical possibilty to actually use JTAG/D2XX and UART on same FTDI chip on linux.
To all - please do not blame Microchip/Microsemi, or Future Electronics or Lattice on this issue, it is not related to those companies, the problem is deeper in the FTDI/Linux system.
br
Antti