Large hidden hole in duct

The hole is in the return duct and looks to be 6 or so inch diameter. Probably an installation screw up. Looks like you have a natural draft (water heater?) flue in the room too, so for safeties sake go ahead and patch it, I don't think eliminating that small of a hole will screw up your return air flow.

Looks to me when the furnace was changed to HE during a basement remodel or whatever upstairs, someone decided to remove a 6" round from somewhere. Probably cut the panel on the bottom to get at the collar above. Cover it with sheetmetal and wipe off the dust so your tape sticks. You probably first want to double check your whole return capacity just to make sure a lot of it elsewhere hasn't been reduced, or that you need a return in a basement room other than this mech room.