I just had my old and new Stackoverflow accounts merged recently. Before having them merged, I associated my new account with all the other sites. I went and looked today and found that after the merge I was no longer associated. I clicked on the associate button and was awarded 100 points, again, as I had not associated my old account with anything. I believe this was because of the difference in User IDs.
I'm guessing this will be erased on the next rep recalculation. Am I right?
Otherwise, just reporting a bug.