I think this post may be helpful to you:
When developing migration configs, you need to update the configs, and it's difficult to get the changes within the install folder to re-register, so there are some scripts you can use, and there are some example drush commands.
Basically you can edit the configs with
$editable = \Drupal::configFactory()->getEditable($config_name);
And you can reinstall configs with
I'd take a look at the code in /core/lib/Drupal/Core/Config/ConfigInstaller.php in the installDefaultConfig function. You could probably use part of that code to update just the config you need to update without touching the parts that should stay the same.