Copying Prefabs Issue

I'm running into strange behavior when copying some prefabs when in the editor.

I've attached a video and will explain also in hopes someone knows whats happening.

I run my game with the highlighted prefab and all works great. It functions as instructed. But if I copy it, delete the old one and hit play functions appear fine but the entire script does not run. However if I save the scene reboot all works.

I suppose it could be the script but I've never seen prefabs not copy data exactly while in the same scene. there must be some form of caching that is being skipped and a reboot fixes it.

Any help would be much appreciated

Update: A section of my script checks for certain requirements was inside a loop when it was meant to be triggered after the loop. Not entirely sure how it worked to begin with but I'm not going to waste any sleep on it...

You can delete this post as it's probably missleading any not helpful for anyone.