If the user account in question was attached to an existing Employee object, it's because of the search criteria and Employee assignment configuration, as per the below.
Assignment of Employees to User Accounts during a sync is based on the following configuration parameter: TargetSystem\ADS\PersonAutoFullSync.
For more information on this, please refer to the Identity Management Guide, Configuring Automatic Employee Assignment
The criteria for automatically assigning Employees to user accounts is defined in Manager for the domain, e.g.:
For more information on this, please refer to the Identity Management Guide, Search Criteria for Employee Assignment
If a user account is deleted in the target system, Active Directory, for example, then depending on the synchronization configuration, the ADSAccount will be deleted in Identity Manager as well. The relevant setting in this case is "Objects Only in Identity Manager", e.g.:
If "Only mark objects, do not delete" is selected then objects (user accounts, for example) are not deleted in Identity Manager, but labelled with the status “pending”.
For more information on this, please refer to the Identity Management Guide, Synchronization Behavior for Selected Items
When an ADSAccount is deleted in the database following a sync, the Employee account will NOT be deleted, by default. Thus it must be deleted manually, or processes put in to place to delete the Employee account, if this is the desired result.