If the user account in question was attached to an existing Employee object, it's because of the search criteria and Employee assignment configuration. Assignment of Employees to User Accounts during a synchronization is based on the following configuration parameter:
TargetSystem\ADS\PersonAutoFullSync.
For more information, please refer to the Identity Management Guide,
Configuring Automatic 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 that are only found in
One Identity Manager" in the Processing section of the User workflow. However, the default setting is to mark the account as "Outstanding", e.g.:

If the desired result is that User accounts should be deleted during a synchronization, the settings should be changed accordingly, e.g.:

For more information, please refer to the
Target System Synchronization Reference Guide,
Deleting objects in One Identity Manager.