Hi,
"So you are saying to change Quartus bank voltage to 2.5V and assign LVDS25? The datasheet specifications on the recommended bank voltage has a maximum of 2.625V (for VCCIO 2.5V) how do you know this will not damage or shorten the life of the part? I would assume the LVTTL/LVCMOS would stay at 3.3V with an actual bank voltage of 3.3V, but are there parts that could get damaged if it is expecting 2.5V I/O?"
As stated, operation is beyond datasheet specs, so I can't guarantee anything. I just mention that it's possible in practice.
Related to output operation, assigned I/O standard is a rule which output transistors out of the available set with different area are activated. With 3.3V actual supply, only smaller current strengths should be enabled although nominal 2.5V VCCIO would allow for larger values. That's particularly important important when driving heavy loads, either resistive or capacitive. IBIS files tell about expectable loaded output current of different I/O standards. Based on this information I conclude that there's no specific risk of operating a 2.5 V output standard with low drive strength at 3.3 V VCCIO.
Related to differential receiver operation there's no useable info in datasheet or device handbook. I can tell that it works, I didn't yet experience damage in 3.3 V operation. Measured common mode range is 0 to 3.3 V, but I don't know worst case margins. Specifically I don't know if there's anything inside the differential buffer that might be overstressed with 3.3 V supply but I won't expect. Surely devices are not production tested under this conditions, so you can hardly expect an official statement approving this operation.
Best regards,
Frank