changing FPGA cyclone4-115 with another one on the same PCB card

To determine what actually happens, you would need to supply a variable input voltage to one of the "migration" related pins and check, if you are able cause a rise of supply current when traversing the undefined logic level range. My assumption is however, that even if the input buffer isn't disabled, the excessive current consumption will be moderate, not above a few mA, and can be tolerated.