[Plugin: WordPress Automatic upgrade] Does this plugin keep custom template changes?

Hello! I’ve been putting-off upgrading to 2.5 because I’ve done so many changes to my WordPress blog that I just can’t take the risk of losing it. But, I really want the ability to do all the new things 2.5 can do.

So, this plugin may be my perfect solution.

But, I was wondering:

I know this deactivates and reactivates all plugins, backs everything up, and even backs up the database, but what about my custom template?

I spent HOURS doing my custom template and all of my custom headers, footers, etc. I just can’t afford to lose all this stuff.

Does this plugin just overwrite those files, or does it account for the changes made to the templates and Page/Post template files?

Thanks for any help in advance!

~Jim