“Managed Deletable References Detected ” should be "“Managed Deleted References Detected ”
As single letter change in the error message would have saved days! And it had nothing to do with Protectable Components in the Base package.
We learned from Salesforce support that we referenced fields of custom objects of the BASE package in a fieldset in the EXTENSION package. We deleted those fields from BASE in a previous release and already upgraded the packaging org of the EXTENSION.
We deleted (and erased) those fields in EXTENSION. Then the error messages was gone and we could upload.
UPDATE: Salesforce just improved the UI in a case we opened and is now showing the problematic components. This makes this kind of error fixable in a second.