Just a note - If you have enabled the JTAG pin sharing option in MAX10 devices for internal configuration without assigning the 4 JTAG pins as single-ended I/O pins or voltage-referenced I/O pins, the JTAG pins will become unused I/O and will default to input tri-state in user mode and thus will not function as dedicated JTAG pins. In this case, the Quartus Prime programmer will not be able to access the device over JTAG.
There is a solution record for this here:
https://www.altera.com/support/support-resources/knowledge-base/solutions/rd05192016_963.html but the workaround is not accurate and will not give you access to the flash. One method that does work is this:
1: Pulled conf_done low and cycle power
2: Program the device with an SOF image that does not have JTAG sharing option on
3. Without cycling power, lift conf_done, and program the new POF file into flash
