We've had the situation now where a customer implemented Sitefinity with an existing design after which we started with their new design.
The old site was quite small and outdated so the requirements in terms of Content Place Holders was quite small. When we implemented the new Master Pages there were obviously a number of different CPHs around with totally different IDs from the previous version of the site. However, much of the content actually stayed the same. The problem is that when you change the master page the content that used to be in old containers just dissappears.
What about popping up a message box notifying the user that many of the controls on the page will be lost of (or hidden) by changing the Template... Would they like to move the following items to different Containers. Then allow the user to select where controls should be placed if there are no equivalent containers on the new template.