Perhaps after this incident, Rumple does something that keeps Pan on lockdown in NL, which is why now only his Shadow, (assuming it’s Pan’s shadow) can leave.
I think that Rumple is the one who rips Peter Pan’s shadow off of him, which might render PP unable to fly himself. Maybe?
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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