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I've worked in WordPress quite extensively, but never did much porting. I've just ported a WordPress install from a .org domain on an old server to a .com domain on my own server (VPS). I did a search and replace as well as ran the neat functions.php file trick explained here: http://www.siteground.com/tutorials/wordpress/change-url.htm.

It was only after the fact that I discovered that the original developer was using WordPress MU and things seem to be a tied to yet a third domain. (In real life the third domain forwards on the front end to the old .org.)

Pretty much everything seems to be working with the exception that when a new user is signed up, the activation link does something funny: it lands on the appropriate .com wp-activate.php page, but once there, the links for View your site and Login are pointing at the third domain rather than the .com. I can't find anywhere in settings why this would be the case, but I'm guessing it has something to do with the activation key. Unfortunately that's an area I know absolutely zero about.

The other thing is that in the Site Admin > Blogs listing ... the only blog is listed at the third domain. I think that means that despite all my changes in both the database file and the php files, the blog thinks it's on that third domain. Not sure how that's possible, but I'm guessing it's an MU issue.

How do I disassociate the new .com site from the third domain? Is there a reasonably easy way to strip this blog out of MU, or is that even advisable?

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I'm not sure but if you're new blogs are showing a link on the wp-activate.php page then that will give you a clue in the code that is creating a link to the third domain. –  1.21 gigawatts Feb 17 at 10:41

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