I sent a personal reply to your message, but it came back undeliverable
because of a full mail box. I said, in part:
I think you are actually a little confused here! Service records DO EXIST
for soldiers in HM Army Regiments who RETIRED TO PENSION. It would seem
highly likely that if your man was discharged due to illness that he was
indeed discharged to pension. As such, there should be a record in series
WO97 at the National Archives.
There are 37 John Baker's in WO97!
Your man's reference is WO 97/603/22
Born WALCOT, Somerset
Served in 46th Foot Regiment
Discharged aged 40