Nothing is deleted unless you asked for it. Delete all data on uninstall, under Setup → Advanced, is off by default, so removing the plugin leaves your setup in place and a reinstall picks up where you left off. Switch it on if you want a clean removal. WooCommerce's own Hide shipping rates when free shipping is available is left as it is either way, since it is WooCommerce's setting.
Still stuck? Ask the developers who wrote it. We aim to reply within one business day.
