The defender had only extended his loan for the rest of the season last week but with The Toffees having mounting injury concerns, Clarke has returned to Merseyside.
It means the England Under-21 international will miss The Valiants' final match of the season at Bristol City on Saturday, with the club safe from relegation following their 5-1 demolition of Huddersfield Town last Saturday.
"Clarky's done a great job for us, he's one for the future. We wish him all the best," manager Brian Horton told the club's official website.
