The magic of comics!
(Also, Wolverine loves the Phoenix, not Jean–he just gets confused.)
Phoenix’s memories (including Jean’s memories which she had absorbed on the shuttle) were shunted into the mind of Madeline Pryor at the moment she killed herself in X-Men #137.
When Maddie finally realized she was a clone of Jean created by Mr. Sinister, she regained access to those memories, whereas before she had been a sleeper agent with a very vague knowledge of her own past.
This all came to a head in the Inferno Crossover, where Pryor threw in with the demons of Limbo to become the Goblin Queen and take revenge on the X-Men for inspiring her meaningless existence. Jean Grey defeated her, and incorporated her memories into her own mind. Consequently, Jean now remembers everything Phoenix and Maddie experienced between X-Men #100 and #242 or so.
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