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I've done some searching and there doesn't appear to be a method of migrating old 2003 based profiles to the new "V2" profiles automatically. Specifically, we're interested in retaining the <Profile>.NK2 file in Outlook, the Favorites folder, and the Signatures folder.

I'm in the process of writing a fairly complicated migration script that'll be executed at login, but seems like this is something that I shouldn't have to do.

The User Migration Tool appears to only work for Vista, not 2008 R2. Any other ideas?

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up vote 5 down vote accepted

Nope. There isn't a way to migrate profiles from W2K3 to W2K8, they're not interchangeable and they're not interoperable. It's a headache but there's no way around the fact that you're going to have to manually copy the components you want (NK2 files, signature files, Favorites, etc.) from the old profiles to the new profiles.

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Caused me physical pain to mark that as the accepted answer. Gotta love Microsoft sometimes. –  gravyface Nov 28 '11 at 18:47
Yeah, I've looked high and low for a way around this but haven't found anything. I've got 600 W2K3 profiles to migrate to W2K8. –  joeqwerty Nov 28 '11 at 18:57
I can post up my ghetto script when I'm done if you're interested. Will be going live with 60 profiles later this week. –  gravyface Nov 28 '11 at 19:06
I would be interested. Thanks much. –  joeqwerty Nov 28 '11 at 19:33
Did yourscript work? Im also in the process of moving 200 users from a TS2003 farm, to 2008 R2. It'll be painful to migrate without the favorites, signature files etc :\ –  user105355 Dec 28 '11 at 21:07

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