I had a similar experience with my hand-coded pages being nuked by Frontpage users at work some years ago. I just kept my own copies, and made all my changes to those. Anything that had been touched by Frontpage wouldn't get updated, it became a dead branch.

I would bring in changes that had happened in Frontpage, but from scratch by hand, not by importing any of Frontpage's code.

I also worked on my boss by setting up an internal A/B comparison site, where internal users could choose which page they liked better. They voted on whichever they liked, with no indication to them of which page has hand-coded and which was worked over by automated tools. When I had over 800 votes in less than a week, with 95% voting for the hand-coded pages and _all_ the user comments saying why they preferred them, I was able to get my boss to agree to keep the tools off my hand-written code for all but a couple of pages in the site.

I also wrote some scripts to generate new pages that were maintainable where there was a need to create new content on the fly, eliminating one of the big excuses for the Frontpage nukes ("You were out of the office, we had to post, and all they know is Frontpage!")

Good luck!