I too have the jtag uart still present, but would like to get rid of it too in the future.
I have written a couple of bash and bat files for update puposes.
Inside Quartus setup a quartus programmer *.cdf that uploads your project to the fpga. now from the bash execute that *.cdf to upload your design and have a working nios inside your fpga. after that you can start the normal flash progammer.
after this just execute the cdf again to restart your design, as there is no other restart feature available when using flash programmer. only cdf does the restart. i have already requested such a restart feature at mysuort.
but i do not know if this flow works with no jtag uart present.
btw : i also would like to know what software is stored inside the jtag uart. i only know that some altera doc recommends to have the jtag uart and epcs available
Regards.
Michael