Drupal 9

In composer.json add to the scripts section. See below:

"scripts": {
    "pre-install-cmd": [],
    ...
    "post-drupal-scaffold-cmd": [
        "patch -p1 < patches/my-htaccess.patch"
    ]
},

Update a UUID: 

drush config-set "config.name" uuid "a2afbb3b-d34f-42fd-bf0c-593a103aa6f4"

Also how to generate an new UUID:

drush php-eval "echo \Drupal::service('uuid')->generate();"

Notes:

• Remember to back up your database first!
• Check your config: 
  • drush config-get "config.name" uuid