When this error occurs, all warnings and code errors disappear from view. The auto-complete stops working too, and you need to close Visual Studio Code and reopen it.
Reload VS with the command Ctrl + shift + p and searching Developer: Reload Window
I saw this message after moving a file from one folder to another, renaming and committing everything to git.
The Visual Studio “Problems” window showed an issue with the “deleted” file. Somehow VS had left a window open for the original location of the file and in it’s tab the file was labeled as “deleted”. Closing that tab in VS got rid of the “Contains emphasized items”
UEFNVS Code does not use GitHub, but does URC Checking in changes help