Packaging error: graph is linked to private objects in an external package: RootComponent

I’ve been trying to package my project, which worked quite some time ago. However, now, whenever I try to package, it gives me an error because some file can not be cooked and saved.

The actual error message in the log is :
UATHelper: Packaging (Windows (64-bit)): LogCook: Display: Cooking /Game/Levels/JFactory/JFactory → C:/Users/xxx/Documents/Unreal Projects/xxx/Saved/Cooked/WindowsNoEditor/xxx/Content/Levels/JFactory/JFactory.umap
UATHelper: Packaging (Windows (64-bit)): LogWindows: Error: Windows GetLastError: Error: Windows GetLastError: The system cannot find the file specified. (2)

In the log file found in appdata, I found some more specific description as to why:
"Can’t save C:/Users/xxx/Documents/Unreal Projects/xxx/Saved/Cooked/WindowsNoEditor/xxx/Content/Levels/JFactory/JFactory.umap: Graph is linked to private object(s) in an external package.
External Object(s):
RootComponent

Try to find the chain of references to that object (may take some time)?"

I’ve tried deleting the files in question just to see what would happen, but then it would simply complain about other files instead.
At first it was a simple actor component, after that one three levels in succession. Also, I do not know what kind of RootComponent this could refer to. A blueprint actor component is pretty standalone as far as I know, so I do not understand how it could reference some “external object”.

I’ve been debugging this for hours now and I can not seem to find the cause. I guess the “graph” is the reference viewer? I have not found anything suspicious though.

Here the cook log with the specific problem:
link text

Here the UAT log with the call stack
link text

EDIT:
I found some more relevant information: It seems to have some relation to a C++ scene component which has a USphereComponent named RootComponent. However, even after renaming it, deleting all visual studio generated data etc., the same error persists.