Yes, Tymeshift automatically updates your user list set in Zendesk every 24 hours. You can refresh the list at any time by going to Agent Permissions 
and clicking on Refresh Agents 
on the top right corner.
Note: suspending or downgrading users in Zendesk to an End User role will automatically remove them from Tymeshift. If a Zendesk user doesn’t need Tymeshift access, you can deactivate them in Agent Permissions page.