Programmatic Reset/Reconfig of Cyclone FPGA

You want to look at the ALTREMOTE_UPDATE megafunction. Using it you can pulse the nCONFIG signal internally via logic to reboot your device.

Document here: https://www.altera.com/literature/ug/ug_altremote.pdf

(https://www.altera.com/literature/ug/ug_altremote.pdf)

There is also this global option: set_global_assignment -name ENABLE_NCONFIG_FROM_CORE ON

However, if you look in the Altera Quartus QSF Reference that describes this variable, it says nothing about how to use it, or what happens when it is set ON vs OFF.

Maybe some Altera Guru has better insight on what this assignment does and how to use it.