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In your file I read :
set_global_assignment -name RESERVE_ALL_UNUSED_PINS "AS INPUT TRI-STATED"
Is this a recommended design rule for Altera boards ? I was suspecting something like that (that I didn't apply).
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Yes, absolutely.
If you do not have this setting enabled, and Quartus defaults to driving unused outputs to ground (as it used to in earlier versions), then you may cause damage to your hardware.
I typically create a top-level design that has all pins used on the PCB. If I do not use a particular interface in a design, then I drive the unused interfaces appropriately, eg., deassert chip selects, drive resets to unused devices active, etc.
Cheers,
Dave