I've reproduced this both in my personal world, and in a new world that I can provide if need be which is currently in this state (screenshot comes from that world). I would upload it but it's too large.

Steps to repro:

• arm yourself accordingly, find the stronghold, get to the end and kill the dragon.
• go back to the end and add the end crystals to respawn the dragon
• after a couple of the towers are reactivated, quit
• restart the game

You are now stuck with no way out.

In my personal world, I gave myself 4 more crystals and destroyed the ones that were stuck and replaced them and it started a new cycle which I let complete and then things were normal again. But if you are in Hardcore, you might be stuck forever.