Drupal is not aware of config_directories['vcs'] in most cases

As detailed in https://support-acquia.force.com/s/article/360005216614-Acquia-vcs-config-directory-vs-Drupal-8-sync-directory, the Acquia platform defines a "vcs" config directory type in addition to the default "sync" directory. It is important to note that the "vcs" directory is not known to Drupal core and most contributed config modules. Config_split is one of the key modules to keep this in mind for. 

Acquia's recommended workaround for this is to set the "vcs" and "sync" directories to be the same in settings.php. This can be done with the following line, for Drupal versions below 8.8.0:

$config_directories['sync'] = $config_directories['vcs'];

The code is a little different for versions above 8.8.0:

$settings['config_sync_directory'] = $settings['config_vcs_directory'];

If you use Acquia BLT with the included configuration settings, this has already been done there.