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  • 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