Does leaving a flat for months damage the wheel?
Leaving a flat for months won't damage the wheel assuming the flat is the only factor in the equation.
If the tire going flat was part of a chain of events there might be damage.
If the tire was sitting in a half inch of water, the tire went flat and the steel wheel was now sitting in water the rim might rust. Even in this example I doubt the rust would be bad enough that the wheel would be unusable.