You converted a structure element from the type Structural (.htm) to Static or Dynamic (.ascx). After deploying the new code the existing pages with the element added cease to work (they show HTML source code from the ascx-file instead of processed HTML).
Type of the structure element is stored with every instance of the element in the database, and this is not changed accordingly.
Change the entries in the DB manually.
In the table AxStructureElement search for the records with ElementTemplateID matching your element ID (from CmsSite.xml). Change Behaviour from 1 (Structural) to 2 (Static) or 3 (Dynamic). Use the SQL statement similar to this:
SET Behaviour = 2 /* or =3 */
WHERE ElementTemplateID = [your ID]