I found the problem myself.
When you define disallow file edit and mods
define('DISALLOW_FILE_EDIT', true);
define('DISALLOW_FILE_MODS', true);
and the plugin auto-updates is still active it will delete the files and try download the updated ones. Since there can’t be any changes, it will stop and then break the plugin.
Found this plugin to manage updates, when you have a local development environment
Easy Updates Manager
https://wordpress.org/plugins/stops-core-theme-and-plugin-updates/
