Why didn't dog's eyes get better after prescription meds?

My dog was diagnosed 4 years ago by a vet eye specialist to have a strange disorder where her body does not recognize her eyes---so does not send any defense to protect their immune system. She has had a drop of prenisolone acetate in both eyes once a day. Two weeks ago her eyes got red and runny (clear watery discharge), and she squints. I called vet and he said to increase drops to twice a day--it did not improve. I took dog to vet and he gave triple ointment---after 4 days things improved---I took to vet and he suggested giving meds once a day. Within two days it got red again. I am giving the drops and ointment 3 times a day now, but plan to call vet tomorrow. Do you think I didn't give ointment and drops enough time? What else could it be? I am worried that after so many years the prednisolone has affected the immunity to her eyes---is there anything they will be able to do---she is 9, and her eyesight is good. No scratchs, no ulcers.