The Pilgrims had agreed a deal with parent club Chelsea to keep the precocious midfielder at Home Park until January 22.
However, the Football League viewed the deal as a new signing and refused to accept Clifford's registration because Argyle have been made the subject of a winding-up order.
The Irish Under-21 midfielder made eight appearances for Peter Reid's men, where he has been on loan since October.
Source: PA
Source: PA