Each time you pass through an end gateaway with an ender pearl from the main island a new portal is created but not vice versa.
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Cannot reproduce. I went through this end gateway three times from the main island with no success of reproducing your bug.
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Can confirm. I had it occur after going through 3 or 4 times, but then could no reproduce it with further testing in a newly created world. Does not seem to occur consistenly and not quite sure under what conditions it is triggered.
[media]
I wonder if MC-272622 is related at all.