Simply right click the files/folders and include them to source control again.
This usually happens if people check in new files/folders but do NOT check in the updated project file, too. The project file contains a list of all files which should be included within the solution. If this runs out of sync, exactly this crap will happen... ;)
Simply instruct your folks to properly check-in. Or do code review on check-in and verify that the project/solution file(s) are also checked in.