I have created a template xxx.dwt.php which links to a mysql database to automatically fill in some fields but applying the template to a webassist page removes the dynamic link.

I created a template that uses a mySQL database to automatically load data to certain areas of the webpage from the database. Template is called xxxxxx.dwt.php
The code for the link to the database and data retrieval is before the opening html tag and the closure of the database link after the closing html tag.
If I apply the template to a newly created page there is no problem and the page works as expected. However if I create a web assist page using DataAssist then when I modify the page by applying the template the initial and final php sections are not present.
Is there a simple way to change this rather than have to update all web pages by hand?

The only solution is to either edit it by hand or to use Framework builder and Themes rather than traditional Dreamweaver templates.

One limitation of Dreamweaver templates is that you have to decide whether you want to have server side code in the template or on the page and you can't have both... so you basically can't have it on the template because you typically need it on the pages. The webassist Framework builder resolves that issue as well as other issues with Dreamweaver templates.