Providing that you use the good tool, it can be very easy to upgrade from an older and modified version to a new version.
A good tool allows you to:
- edit files remotely (using ssh, sftp, or ftp).
- diff 2 files, and merge differences selectively.
On Mac OS X, you can use BBEdit (non-free) or Text Wrangler (free), and I think TextMate (non-free) will do it too.
Alternatively you can use a good FTP client, that will allow you to edit files via a external editor, so that you can make a diff between your files online and the new version on your hard drive even if your text editor does not support remote editing.
If you compare every single text files in dark-matter (js, php, css, html, txt), it takes about 10-15 minutes to review all the changes and commit them on your modified version online. If you compare only files that have changed, it should be done in less than 5 minutes.