In this issue Psylocke says that when Proteus "died" his energy dispersed all over Muir Island, he was kinda trapped between life and death that way.
So my theory is that when Wanda created the House of M, history changed so that that never happened and Proteus left with the Exiles. And when HoM, Wanda put everything back to how it was before (with the exception of "No more mutants", Muir Island was once again saturated with Proteus' being even though he had technically left.
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In this issue Psylocke says that when Proteus "died" his energy dispersed all over Muir Island, he was kinda trapped between life and death that way.
So my theory is that when Wanda created the House of M, history changed so that that never happened and Proteus left with the Exiles. And when HoM, Wanda put everything back to how it was before (with the exception of "No more mutants", Muir Island was once again saturated with Proteus' being even though he had technically left.