Deleting an employee removes them from your account completely and is not reversible. If you want to add them back at a future date, a new profile will need to be created and they will have to go through the invitation process again. This option is best for employees who are no longer employed by your organization and will not be returning. Shift history and time sheet history is retained, however.
Deactivating an employee keeps the user's info in your account, but prevents the user from logging in or receiving notifications. This is a good option for seasonal employees, those who might go on extended leave, or employees who may be eligible for rehire in the future. The employee can be reactivated at any time without having to go through the invitation process again. Premium and Business users are not charged for deactivated users.