If an employee has a shift for a day and you need to record an absence you have several options:

If you choose to link the WHOLE shift, then the entire shift will be removed from the time cards.

If you choose to link PART of the shift, then the hours entered will remain as the shift.

For example, you have an employee scheduled Friday from 8a-4p (8hr shift). In the morning they call in their child has to go to the doctors and they need to take 4hrs off. You can pick to link PART of the shift and leave the 12p-4p part of their shift available.