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First you may want to check in the pinout file of your design what's connected to the LED pins. It may be the case, that unassigned output pins of your design have been connected to these pins.
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Do you mean the .pin file? Yeah, it shows that many of the outputs in my block diagram have been assigned to random I/O pins, but they show up as unassigned in the pin planner. It's absurd that quartus would do such a thing, since there is lots of hardware connected to these pins that could potentially be destroyed by this. Is there a way to prevent this, besides manually assigning every single pin?
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