After the project is completed in your org, you should mark the Project as Inactive from the Projects list. So that the users don't see them in the drop-down list for the Check-Ins.
To remove/deactivate Projects from the list
- From the Salesforce Admin ID, go to the Projects Tab
- Click the Edit button for the Project that you wish to mark as Inactive
- Click the Inactive check box and save it,
The users will not see the deactivated Projects in the Projects list. This also shortens the list of Projects shown for the Check-Ins.
Note: Follow the same instructions for marking the Worktypes or Tasks as Inactive in your org. Or any objects that are set to track time to.