I heard of infections causing Autoimmune disease, i never heard of it completely alleviating, Was it a viral or bacterial?
The only thing i heard is that infestation with certain parasites, can alleviate allergies and autoimmune diseases(the medical community hasn't accepted it).
I think its more of your bodies immune system exhausted itself by fighting the pneumonia than actually redirecting the autoimmunity. Think about this way, in an Autoimmune disorder, anti-bodies are directed against specific parts of your body, these dont go away, because you will also have those tissues that the antibodies can attack. i think your immune system is exhausted from producing antibodies, so there is less in your body to damage your tissue. The exact opposite can happen as well.