Hello! I have systemic sclerosis with secondary raynauds. I too have had similar problems with nails on toes and fingers. I'm told it's due to poor blood supply to the nail bed, which makes sense. The nails are particularly poor on the site of ulcers which I get on the fingertips, and the nail can begin to lift away from the nail bed (not pretty!) At this stage I cover them with breathable dressings until they've calmed down. The nail will grow up and out replacing itself with a healthier version once the blood supply has improved (in my case iloprost infusion or better care over warmth). Hope some of this helps, it is a bit of a battle!
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