You should only use Composer commands to modify the contents of vendor, as it's not just folders but there's also a manifest file detailing all the libraries and their versions.
Run composer install to re-download everything according to the composer.json file. You might need to delete (better to rename to a temporary name) the vendor folder to make sure everything is properly re-downloaded.
In the future to remove extensions you should use the composer remove <package> command.
