The ender dragon can destroy both end portal blocks and end portal frames, meaning it can completely destroy stronghold portals (don't ask how he got in the overworld) and remove the portal from the bedrock "fountains" (aslo don't ask how there were two dragons in the end)
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well instead of proving this issue, couldn't you just change the enderdragons actions or what ever so that when it hites portal blocks it goes through them instead of breaking them?
That would be a feature request, and should be posted on the MC forums here. I personally have no say on the matter.
You begged for asking this questions:
How got the dragon in the overworld ?
How were there two dragons in the end ?
Ok, the overworld was a superflat preset with the biome set as "sky". There were also strongholds in the world, as well as an ender dragon, which destroyed the portals in the strongholds. In another world, i had already slain the ender dragon, but i spawned another using a spawner, and it destroyed the portal part of the bedrock fountain, leaving only the bedrock shell and no portal
See though I believe this issue exists, I doubt anything would be done to change it. To solve many AI problems, the Devs decided to have the dragon fly through and destroy anything in its path. By modifying the game files, you're creating otherwise unachievable problems, which would likely take an unnecessary amount of work to fix. What I would recommend instead, is to wait for the plugin api, and change the dragon's behaviour yourself. That, or create a mod.