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?
Thing is though that Pan has been shown with his shadow attached, (you can see it clearly in his final scene with Henry is 301), so I think that if the Shadow is actually Pan’s shadow, he still has control over it, which he probably wouldn’t if it had been forcibly removed by Rumple.
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