There are a few factors that should be considered when a user’s department is changed or a new department assigned (In between a timesheet period) as any timesheet that has already been created/generated will be based on the user's old department.
 
The following behavior would reflect in Web TimeSheet:
  • The user would not be able to see the tasks (for the new department) that were assigned through the department right away
  • If the user is assigned directly to a Project Team or task (rather than as part of a department assignment), the assignment will remain intact, even if the user's department is no longer included in the departments the project is visible to.
  • Reports filtered by using the new department will not show data for these users
  • The historical data is not affected by these changes.
  • Users will not be automatically added to the Projects which have the new department already assigned to them and hence can't select the projects from his new department, on the timesheet. 
Steps to avoid these issues:
  • Assign the User to the tasks within the project rather than assigning departments
  • If a new department has been assigned to the user along with the old department, delete the timesheet of the user and recreate a new timesheet for the same period (From Historical Timesheets)
  • If a user has been moved from one department to another, create 2 manual timesheet periods and assign it to the user. The first would be for the time period in the old department and the second for the time period in the new department, until the next timesheet period starts. Then delete the historical timesheet and regenerate the timesheet.
Note:
If you want to determine the departments that are linked to timesheets, go to Historical Timesheets. This list will show all the timesheets, as well the user and department(s) linked to the timesheet.