For our search index functionality we use Lucene, which will create the search indexes in a physical folder under ~/App_Data/Sitefinity. The index will also preserve the information about the "default page where X is published", and each time you re-index the old index files are being replaced with the new ones, which might explain why you had references to the old domain before re-indexing the published site. So to answer your last question, no, you are publishing your site normally, I guess like more than 90% of us do it.
All the best,
the Telerik team
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