I've run into this several times now. I had hoped that it would be fixed in CU4 but it does not appear to be. Here is my scenario: I have a Software Update Group named
Windows Server 2008 R2 Updates - 201503
The updates have been deployed into a Deployment Package named
DP - Windows Server 2008 R2 - 201503
(I had been packaging them into yearly packages but you'll see why i don't do that anymore in a moment). I have had some of these updates either expire or be superseded so I need to remove them from the Software Update Group. To do this I am selecting them, going to Edit Membership then un-checking any groups they are in.
Now here is the part that makes me ... dissatisfied. Once I do this if I check the content status of my Deployment Package it now says
The source directory "\\SCSM_SERVER\Updates\Windows Server 2008 R2\2015\03\bb97ff2f-4eb4-48b0-bf0b-096ee3bcb89b" for package "AAA00098" does not exist" ...
Anyone know how I can get it to stop from deleting the entire deployment package when I remove a couple updates? Or is there a better way of handling this scenario?