After we imported content form the old catelog before the upgrade, all the catalognodeex tables are empty.
So pre episerver 10, we have a catelog export as the zip file. we deleted the catalog from commerce. We then re-imported the catelog and now all the tables prefaced by "CatalogEntryEx" are empty. Is this expected?
Yes that is expected. In Commerce9 the CatalogEntryEx and CatalogNodeEx tables are no longer used. If you want to check for data, look at CatalogContentProperty. However, keep in mind that Episerver does not guarantee backward compatibility on database schema.