Cause

A part of a project was filed off as a subproject <x>. Subsequently a further subproject was filed off from this filed-off subproject. When the subproject <x> is restored into the original project, it is subsequently deleted. The project filed off from the subproject <x> is retained, but can no longer be restored.

Solution

1. Start any check run in order to delete the message.
2. Restore the subprojects in the reverse order in which they were filed off.