After leaving The End (either by being killed or entering the escape portal), I was put back to the bed in the Overworld properly, but right after the intergrated server thread froze for 2 minutes (client side was still smooth, I could move, place, break,... but the server wasn't responding). After that the server got back to running as normal.
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I'm having the very same issue right now, however I did not try to wait 2 minutes. Reloading the map did not help and I'm currently stuck in the End Portal. (I.e. I get teleported to the overworld and then the server freezes.)
I didn't run two instances of MC, but at a time when the server was freezing I quit and rejoined the world. Might be the old server thread was not closed.
Where you running two instances of the server on the same world?