Yes, the POR circuitry will continue to monitor the POR monitored power supplies of Arria® II GX devices and Arria II GZ devices after entering user mode.
For Arria II GX devices, these supplies are VCC, VCCA_PLL, VCCCB, VCCPD, and VCCIO for I/O banks 3C and 8C.
For Arria II GZ devices, these supplies are VCC, VCCAUX, VCCCB, VCCPGM, and VCCPD.
If any of these monitored power supplies goes below their respective POR trip level, the POR circuitry will assert the POR signal and force the device into reset.