A quick SEO myth buster post for you. You know how you can set the preferred domain in Google Webmaster Tools? Well, if you do that, you won't be deindexed, so don't worry.
A webmaster asked this question in a Google Webmaster Help thread and Google's JohnMu replied.
No, setting a preferred domain name does not result in a site being deindexed.
It is hard for Google to be more straightforward than that statement.
Forum discussion at Google Webmaster Help.