Config split settings file generated into split directory Drupal 8.7
I have a multisite split. The config_split.config_split.&lt;sitename&gt;.yml files are supposed to go into the config/default directory. For some reason when updating a split on one of my sites, instead of updating the existing file in that location, it creates a new file in the config/sitename directory. It only does it on this one site. When I compare the newly generated file to the one for that site in the default directory, only the new changes are different. The rest is the same.
Have you checked the $config_directories array in the settings.php/settings.local.php files.

It might be a good idea to explicitly set it via config as per https://www.drupal.org/docs/8/configuration-management/changing-the-storage-location-of-the-sync-directory:

$config_directories[CONFIG_SYNC_DIRECTORY] = '../config/sync';