When you delete an item that Team Foundation Version Control expects to exist on-disk, it detects that deletion and displays that as a "detected change". Note that this is merely an informational message. It is not a "pending change" and it cannot be undone, nor can it be checked in to the server, at least not without promoting the detected change to a pending change via a call to tf delete
.
However, if you're worried about accidentally promoting that change, or if you're just tired of seeing it, you can instruct the client that you shouldn't have those in the first place. The easiest way to do this is to do a get on that path of a previous version that didn't have these files, namely changeset 1:
tf get /version:C1 $/PROJECT
Now your local working folders are in sync with your workspace mappings and there should be no more detected changes to $/PROJECT
.