Sorry Density, but your post is confusing. A grommet is a small washer placed in the eardrum so the fluid behind the drum in the middle ear can escape. It is due to failure of the drainage tube / chronic infection etc.
Autoimmune disease includes many illnesses. Deafness is normally from the inner ear
It suggests you have two separate problems, so you need to discuss this with your ENT surgeon to clarify and if so which is causing what !!! I doubt even a CASA will stop you flying with a grommet other than immediately after the 'operation'
However many autoimmune diseases do cause tracheal stenosis although in practice we do not see these patients needing operative management. In fact it is very rare. Surgery is normally only performed for symptoms such as breathlessness. In practice you would lose your medical from the stenosis way before needing surgery. If you become breathless that will be of interest in your medical, otherwise I cannot see it is an issue. BUT these diseases effect many other systems so you would be best advised to talk to the specialist looking after the autoimmune disease itself and learning of the likely progression / prognosis / issues.
If you have more information eg a specific diagnosis, we may be able to help you further. And I regret I am from the better side of the Tasman Sea so I cant help with specifics for your country.