Have you ever had the problem with editing files offline or outside of Visual Studio only to find these files are neither marked as added or changed in TFS. Seems there isn’t a good way to fix this in GUI but the following Stack Overflow post specifies a way to do this using the command line TFS Power Tools:

tfpt online /adds /deletes /diff /noprompt /recursive directory-name

This recursively checks through your directorystructure and flags anything deleted, changed or added. Make sure you use it carefully though, in my case it marked all obj and bin-folders as added which was a bit unfortunate. These can be removed using the /exclude flag, however, like in this example:

tfpt online /adds /deletes /diff /noprompt /recursive "C:myDir" /exclude:bin*,obj*

Another tip is using the /preview -flag this allows you to check what files would actually get checked out before applying.

Check this stackoverflow post out for the complete solution.