I guess it depends on your definition of "allowed" vs "required". I believe that in commercial aerospace applications a device change (e.g. change of manufacturing process or process parameters, let alone different masks) would require the entire assembly to be recertified. That's why Boeing procures all spares for the product lifetime up front.

At some point, I'd assume that beggars can't be choosers. If the new chip works and does not introduce issues while still allowing the plane to continue to fly, I'm guessing they'll take the plane still flying.