Hi is there anyway to make this work with the portable vehicles plugin does not let me pick it back up so wondering if it's possable.

Do you know the precise reason why you cannot pick up miniciopters with the Portable Vehicles plugin? I expect that plugin to provide a message indicating the reason. Also, what makes you think it's related to MiniCopter Options? Most likely, you simply need to configure the Portable Vehicles plugin to allow picking up minicopters.

The reason i think it is stopping it is that it edits the minicopter so maybe it using a dif prefab name.

No, prefab name is not changed.