making changes to a template and uploading those changes are two separate processes.
Dreamweaver identifies pages that are based on a template by looking for the following line on each page in your site:
<!-- InstanceBegin template="/Templates/Main.dwt.php" codeOutsideHTMLIsLocked="false" -->
When you upload files using Dreamweaver FTP, it is not looking for he pages based on a template, it is just uploading the pages you told Dreamweaver to upload.
You have to manually tell Dreamweaver what pages to upload