I think it was meant to tie into his "Wolverine gets killed, resurrected by the Hand, turned into an assassin, Jean goes undercover to save him" storyline.
I always thought it was just Claremont not knowing what to do other than make more angst. Kitty couldn't become solid, Peter was stuck in metal form, Storm lost her powers, Rogue couldn't touch anyone, Nightcrawler's teleportation was on the fritz and Wolverine's healing factor was broke. And of course Cyclops still had his original problem.
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