Am I right in my assumption here that when you change your custom domain, the original feed that gets posts to the Timeline stops working?
When you change your domain name, Micro.blog is supposed to update the feed URLs too… I’ll double-check that there isn’t a bug there. If anything still looks wrong, you should be able to remove / re-add the feed URL under Account → Edit Feeds & Cross-posting.
My blog is also not updating after a domain change. Removing and re-adding the feed URL fixed the issue for a while, but after a few minutes it went back to the previous version without the new posts and with the old theme =S