Используйте доку ".. Device Family Pin Connection Guidelines"
В моей так написано:
When using as optionally open-drain output dedicated INIT_DONE pin, connect this pin to an external 10-kΩ pull-up resistor to VCCPGM. When using in an AS or PS multi-device configuration mode ensure that the INIT_DONE pin is enabled in the Quartus II designs. When not using as the dedicated INIT_DONE optionally open-drain output, and when this pin is not used as an I/O pin, then connect this pin as defined in the Quartus II software.
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