Let's go with the following example:
1. Default project as it is and create a new project and add a link from the Default Project towards the new project (I used RegionMapping, you should use something that depends on other datatypes).
2. Delete the default project. What happens is that the Region Mapping is copied into the new project before deleting the one it was created in. When you want to view the Region Mapping, obviously it won't work because you don't have the Surface and Connectivity.
This problem should be solved because it does not make sense to leave it like this. I think the right solution is to copy the linked datatypes as well.