I used to bite my lips everyday for a year leaving my lips raw and dried out. While I'm not exactly sure what caused my ec, I'm pretty sure the there's nothing wrong with me internally. I'm not gonna get into theories about the cause of my ec or yours for that matter.
To answer your question,
If the dermis (1st skin layer) is missing or damaged, Aquaphor won't do anything except suppress the symptoms. You'll know this if you check your peeling cycle. Does it peel every 3 days? Does the skin turn white when wet? Actually if you see dead skin on the first day (raw lips) forming, then the above statement is true. This is true for most people with ec. If you can fix the dermis, then you're halfway cured.
When I apply aquaphor now, my skin grows back because I think the dermis is healed.
How did I fix the dermis?
I applied a product called Gloves in a Bottle. It would've healed my lips entirely if only I left the product on for longer.
I would suggest you give this product a try. Apply one thick coat on raw lips then leave it alone for a few weeks. It should come off by itself then. You should be able to see new skin within 3 days. If you don't, then it's obviously not working for you or you didn't apply correctly. Just don't take it off or you'll have to start over again.