My Neather Portal Spawn Un-generated?

Created a world. Found a neather portal spawn. Looted its chest. When I passed by after building a base it was gone.

 

Some of the netherite is still there but a square chunk is now missing where the portal once stood. It is definitely the same portal as I am meticulous about mapping out areas, plus its the only portal within the starter map.

 

I also stole the chest by the portal, and I make creative copies of worlds for scouting and backup copies incase of world crashing issues. May have caused the glitch. Idk, just incase the copying world may have caused the issue.