Okay, I'm playing SH4 for the first time in about three years, and I remember that you can heal Eileen's damage by putting a Holy Candle next to her. I've managed to heal her like that in the past as well.

My problem: right now, she is very, very damaged (not even sure how she got that bad, I was very careful) and I've tried placing several candles next to her. She appears to heal all the way every time, but as soon as the candle burns out or we walk away, her injuries begin to slowly fade back in until she is limping more severely and starts crying for mommy again.

Does anyone know what the problem is and how to heal her permanently? I can't remember what to do.

You cannot heal her permanently, I'm afraid. The best you can do is unload all your Holy Candles and let them heal her before you take the smelly box from the superintendent's room. That's the last time you'll be able to heal her before the final boss fight.