The configuration ROM can be controlled by setting nCONFIG to Low and nCE to High on the Cyclone® V device.
https://docs.altera.com/r/dvxWxDO1_JfCNh~DgmxAcw/UZS1FhGDch~hZGHsCJUpCQ
(Please search for Controlling EPCS and EPCQ Devices)
(excerpt)
Note: If you wish to gain control of the EPCS pins, hold the nCONFIG pin low and pull the nCE pin high.
This causes the device to reset and tri-state the AS configuration pins.
--------------------
Category: Programming Configuration
Tools: -
Device: Cyclone® V