I can’t really help you when using gutenberg. My basic understanding is that when using the new editor that all field groups appear in the sidebar. If this was not the case before and it is now then it is likely a change made to WP that is causing this.
Re-saving a field group may not have any affect. WP stores the order of the metaboxes in the _usermata table for each user under the meta_key “meta-box-order_{$screen_id}”
