The configuration ROM can be controlled by setting nCONFIG to Low and nCE to High on the Cyclone® V device.
https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/hb/cyclone-v/cv_5v2.pdf
(search for Controlling EPCS and EPCQ Devices) (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.
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Category: Programming Configuration
Tools: -
Device: Cyclone® V