Added to that idea of Henry being temporarily dead or in a comma is this new episode description:
Henry tries to get Emma to return to Storybrooke causing a crash. Evil Queen/Regina uses her weapon of choice, a poisoned apple, in both Storybrooke and Fairy Tale Land. In Storybrooke, Henry gets caught in the crossfire as Regina tries to rid herself of Emma permanently.
Henry will get caught between an evil plan Regina has to be rid of Emma once and for all. It sounds like Henry may very well be collateral damage. However, I don’t think they’d kill him off permanently.
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"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy