Just some thoughts, which your vet may or may not have considered:
Could it be stress? Have you tried Feliway to see if that helps reduce the scratching?
Or, it could be a reaction to any spot-on wormer or flea treatment you've used? If so, stop using it.
Or, it could be general dehydration and dry skin, which causes itching? In which case, stop feeding dry food and switch to all wet (like Hi-Life pouches).
Or, the cat could be sensitive to something in the food, which brings out scratching? In which case switch to a good wet food like already mentioned.

Hope you manage to sort it out, it can't be pleasant for you or the cat to have this going on!

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