Hi
When you update the template it overrides the custom changes. Also, your site is based on older version of JA t3v2 that does not have custom.css file and local folder.
You have to apply the changes again on site. Please note the template is not ready for Joomla3.8.1 at this time, so kindly restore the backup and wait for the update.
For the department module, you have to publish the module again to make it work. I am not sure what custom changes you applied on it because its no longer showing on your site.
Always take backup of custom changes and site before update Joomla and template.
Regards