I've had this ongoing problem with Subversion with one of my ColdFusion projects. The set up with the client is far from ideal - here's how it works:
I have a Subversion repository for all of the code and I use it for all of my work. When I'm ready to upload changes I export from Subversion and upload either the whole thing or just the changes if there are only a few. Once the work is uploaded to the server the client can download view templates, make changes to them and upload the changes. This allows them to make changes to the appearance of the site without having to bother/pay me. We've been doing this for a few years so the client knows what they're doing and doesn't usually create problems with any existing ColdFusion code in the templates.