When the JTAGEN pin option is enabled in the Intel® Quartus® Prime Software, Intel® MAX® 10 device JTAG pins will become user I/O pins in user mode.
If there are no I/O pin assignments on the JTAG pins, they will be reserved as unused I/O pins and will be set as input tri-state in user mode. Thus, these unused I/O pins will not function as dedicated JTAG pins even though the JTAGEN pin is pulled high in user mode.
If you intend to switch back and forth between user I/O pins and dedicated JTAG pin functions using the JTAGEN pin, you must make I/O pin assignments on all the JTAG pins in Pin Planner to identify the pin direction (input, output or bi-directional) and also the I/O standard.