7.2.4. Assigning Device Pins to Logic Lock Regions
A Logic Lock region incorporates all device resources within its boundaries, including memory and pins. The Intel® Quartus® Prime Pro Edition software does not include pins automatically when you assign an entity to a region, unless the Core Only attribute is off.
You can manually assign pins to Logic Lock regions; however, this placement puts location constraints on the region. The software only obeys pin assignments to locked regions that border the periphery of the device. The locked regions must include the I/O pins as resources.