Force TFS to detect changes
Solution 1:
A Folder Compare (File->Source Control->Compare...) should do the trick. Select the top folder from where to start comparison, and select to compare with Latest Version. The result hould show files that are changed, and whether they are checked out or not.
Solution 2:
TFS has a "Reconcile" command for this. See https://stackoverflow.com/a/22860674/932282 for a complete answer.