Well he first rule is to not make custom changes to anything we supply but always make a copy. So – if you are wanting to make sweeping changes to templates, for example, then make a copy of the theme to make it uniquely yours and then it will be safe from updating. We should have a codex article up on that pretty soon now.
If you just want to make minor changes to an overlay the same applies. Make a copy of the overlay you want to change and make it uniquely yours.
The WP Updater will currently wipe the entire folder and replace it with an updated version. This is a constraint of the updater. The WP team have plans to change this so that we can update individual components but they have not put this in place so we have to use what we have got.
So if you are making changes to one of the themes we supply you need to make it safe from updating so rather than use the WP updater it is better to download it from our site and update it manually.
I’m not really sure there is much more we can do to be honest. We always advise people NOT to customise our supplied themes but we can not exactly force them to do so!

