First, the flea treatments are a good start to eliminate one source of allergies. Also make sure that your house is flea free.
Did the vet give her any medicine, like a steroid injection, oral prednisolone or antibiotics? Those are usually the initial treatments for scabby cats.
If she had been given any of those medications and there was no improvement, then something more significant could be going on, like an autoimmune condition.
Let your vet know that she has not improved.
Please do not scrape the scabs off unless they are about to fall off, you could introduce infection.
Good luck, and keep us updated!