There are various ways to recondition your players and restore match fitness.
1) Place the player in your reserve team for a few weeks to regain fitness
2) Use them as substitutes in games. Regardless if they play to 50% condition it helps
them
3) Arrange easy friendly's and play them the whole game. For fun, see how low they can go.
I got Miroslav Klose to 4% which in my eyes is clinically dead
Remember the more condition they lose in an appearance whilst unfit, the more it will help
them recover