This question on Pro Webmasters was originally migrated to StackOverflow. StackOverflow reverted the migration as off-topic. The only answer to the question had accumulated 90 rep (9 upvotes) before the migration was undone. Those seem to have disappeared. Is this expected behavior?
Yes, this is expected behavior. From the blog post "Reputation and Historical Archives":
So in this case, because the second condition isn't fulfilled, the reputation is lost.
This is intentional, as the lack of reputation loss is for answers given to the site in good faith at a time when the site ran with different tolerances for what is appropriate and what is not.
If someone contributes an answer today with the knowledge that the question (or answer) is not appropriate for the site, the point is that they shouldn't gain reputation for it, as it's inherently not in good faith (we have to make some assumptions about what people do and don't know, otherwise, we'll be trying to reward rep back to everyone who says "oh, I did it in good faith").