Republic of Ireland international Long had looked like leaving the club in a shock deadline-day move to Hull City - but the deal fell through.
Now Clarke hopes that contract talks with the 26-year-old, which have previously stalled, can now resume and reach a positive conclusion.
"The club made a decision which was right for them - obviously I'm part of the club - but very quickly, the bid collapsed," Clarke told the Daily Mirror.
"Shane and his advisor need to sit down and talk with the club to try and get a resolution.
"Given contract talks had stalled for so long, it is possible that's why the club originally accepted the bid.
"Shane is a very, very important member of our squad. I'm delighted he's here."