You discover that content for System Center Endpoint Protection (SCEP) software updates has been removed from active deployment packages. When you try to distribute these deployment packages, the attempt fails with the following error:
The source directory "//name/source/Updates/SCEP/bfdc178c-6e80-47cb-b698-b34dc39b67f4" for package "FCS0012D" does not exist.
This issue occurs when the update package shares the same source location with other software update packages. When Configuration Manager performs a cleanup of orphaned folders in this situation, it doesn't recognize that some of these folders actually belong to another active deployment.
To resolve this problem, re-create the package in question, and make sure that you specify a unique source location. This will prevent content folders from being removed from deployment packages.