When you view pending time off you will see a list of conflicting shifts that will be unassigned when that request is approved. All overlapping shifts will be listed.
You can uncheck any listed shift and choose to keep that assignment if you like. This can be helpful if you have overnight shifts and, for instance, approving Thursday off does not include their Wednesday night shift that goes into early Thursday.
If you uncheck a shift and approve a time off then the employee will be notified of the new time off and they will also be reminded of the shift you left them assigned to if that shift is on a published week.