In the short term, it will certainly cause more uncertainly.
But having a potentially ineligible CinC isn't exactly great for moral. Doesn't do much for "good order" if the top of the chain of command is actually empty. It would be much better if issue would be settled, whichever way it comes out. IMHO of course.
Precisely, Gato. The uncertainty sucks either way.
Colonel, USAFR