I see quite a few related posts in here, but no answers. We've been using
Contribute since version 1 with out clients and recently we both switched to
developing in PHP (from ASP) and to using Contribute CS3. We did not see these
problems with ASP (using SSI) and Contribute 3/4.

On to the issues:
We have now had 3 or 4 clients report a similar problem - once in a while,
when they publish a change to a page, some of the PHP includes are not written
out with the HTML - that is, a header & footer disappear. We can go in with
Dreamweaver and reapply the template, but the client can do nothing but roll
the page back to a previous version.

We finally tracked down what may be part of the problem - the local copy of
the template which is stored in Local Settings/Application
Data/Adobe/Contribute CS3/Sites is wrong. Somehow, Contribute creates a
version of the template that is simply missing the PHP includes. If we delete
the local templates and reconnect in Contribute, the template is re-created
with the code. But somehow, during a random edit, the local template gets
replaced with a bad version.

It begs the question: why is Contribute writing out a version of the template
instead of simply putting the FTP-ed copy of the template in the Sites
directory? And how do we fix this?

The only thing we have found that kind of works is if we have the client
remove their connection and recreate it with the key. The problem is, they
would have to do this daily at the rate we're seeing. Not acceptable.