According to your description, sounds like there is something wrong with your source control binding. Or maybe some files outside of Visual Studio do not detect by TFS server. Which cause your workspace and TFS server out of sync.
If you want TFS server detect changes done to files outside of Visual Studio, the simplest way is using local workspace.
Now anything else changes files outside Visual Studio, your workspace detects the changes automatically.
It also detects adds or deletes but you have to include them to your Pending Changes manually with the link under `Excluded Changes
If you are using server workspace, this is kind like when you are offline, you cannot work with your local files because they are read-only until you check them out. So highly recommend you switch to local workspace, you just need to make sure you open the files in VS from a path which the same as your TFS local worksapce. Then it will auto sync changes in Visual Studio and show in pending changes.
More detailed information on the pros and cons of local and server workspaces, please refer our official link.
Now in your situation, we suggest you fist back up all of your local codes/files first. Then delete your old workspace, create a new local workspace.
Get latest from your sever, then copy all your back up to your workspace folder. Then let windows file system auto detect the difference between them, replace files download from server with your back up local version.
Now your local workspace should contain the latest version of your code/file, Visual Studio will auto detect the changes and list them in pending changes, if something added in excluded list, manually promote them.
Finally you could just check in/push all pending changes to TFS server. Now everything back to the track again.
Hope this helps.