You can get rid of this warning by using the Reset Status option at the project window. First remove the project from the transport. You can do this by clearing the Transport No. at the project page or deleting the project from the transport page.
You now see that the color of the project is grey. This means that the project is transported in this transport but currently not included in this transport.
Now it is possible to click the Reset Project option at the project card.
The Transported boolean is set to false for this project and it got the default status of the project flow. Because the Transport No. of the project is cleared it can be included in another transport.