If you make changes to the ExCM pages and you do a re-deploy your changes will be lost. Make sure you save a backup copy of your changes to any ExCM pages once finished. To eliminate this issue you can make a copy of the original files and make your changes to the copy. If you choose to go down this route you will have to tell ExCM where the new pages are located at. You can do this from the Navigation Url section of the Delegation Settings page. If you have sub-sites that break permission inheritance you will have to update the location of the ExCM pages for each top-level permission site.
If you want to give me a summary of your planned changes I can provide a bit more guidance.