Not yet. We are working on a feature request to edit check in/out times for someone that has checked out.
Unless you meant using a different time than the current time when checking someone into a mission. The answer in that case is yes, you can choose a time in the past to check someone in. Sometimes the command structure with the computers arrives later than the team members. You can get caught up in Mission Manager and check members in using their correct arrival time by editing the Check In Time before clicking the Check In button. You cannot choose a time in the future or they will just be checked in with the current day and time.
If we missed the issue, you can always call tech support at 619-457-6121.