The other day I added some files to my Visual Studio project, which I deleted later, however somehow they were not deleted from within TFS. Now I did continue with my coding of other files etc.. and when it was time to check-in my changes, TFS wanted to check-in the deleted files as well, which was very strange to me, since the files did not exist anymore - the change was marked as "add" instead of "deleted". Due to that I was not able to check-in my other files. To overcome this issue you just need to undo the changes of the deleted files, which will delete the files permanently and allow you to check-in your other files back in. Hope this helps someone.