Hi Mark,
Are you getting any results when you search for terms that are in content on your site?
Check if there are files in the /Data/Sites/[SiteID]/index directory.
Did you try your search more than once after deleting the files in the index directory? The reason I ask is that the index is not rebuilt until a search is performed which triggers the site to check the index and when it notices that the directory is empty, it spins up an index job. If you only searched once, you wouldn't get any results because the index hadn't been rebuilt yet. Once the index is rebuilt (shouldn't take long if your site isn't very large), you should be able to find what you are searching for. The index has undoubtedly been rebuilt by now so you might want to try your search again.
HTH,
Joe D.