The Quartus® II software may direct you to connect a pin to VCCIO or NC when migrating depending upon how the I/O bank and the I/O pins reference the VCCIO in the selected migration device.
If there are no I/O pins that reference the VCCIO pin(s) of the migrating device, the Quartus II software will set the VCCIO pin(s) as NC.
If there are I/O pins that reference the VCCIO pin(s) of the migrating device, the Quartus II software will set the VCCIO pin(s) as VCCIO.
For example, when migrating from a Cyclone® V device 5CEFA5F23I7 to an 5CEFA4F23I7 and comparing both devices, IOBANK_1A does not exist in the 5CEFA5F23I7. Hence, since there are no I/O pins referencing the VCCIO, the Quartus II software will set VCCIO for IOBANK_1A to NC as the migration result.
In another example, when migrating from a Cyclone® IV device EP4CE55F29C8 to an EP4CE40F29C8 and comparing both devices, IOBANK_3 exists for both devices, and in this case the Quartus II software will set VCCIO for IOBANK_1A to VCCIO as the migration result.
This problem is fixed in the Quartus II software v14.1.