I don't know how it works, but I have one configuration in external flash and a different one is downloaded to the FPGA via quartus_pgm ...-i. After the download is finished, the FPGA executes the downloaded one.
I decided to go the "hard way":
-quartus_pgm simple_config.sof
-nios2-flash-programmer complete_config+nios_application.flash
-quartus_pgm complete_config.sof
This way it restarts with the correct configuration.
(I need this 'restart-without-power-cycle' for production programming and testing without operator intervention).
Thanks anyway.
BR
Fernando