As long as your "empty" pages are correctly returning a 404 (or 410) status code, you should not have to worry about any ranking drop in the new domain.
Google will treat the URLs as removed - which they were - and eventually reduce the crawl frequency on them.
A site: search is not a reliable way of showing what is indexed. It shows indexed pages as well as redirecting pages that are not indexed. While URLs from your redirecting domain show up in a site: search for that domain, your redirecting domain won't show up in any normal Google search query.
If you want to see what is indexed on your alternate domain, ...