Recently, a question about the irrationality of $\pi + \mathrm e$ got migrated from Main to Meta. While on Main, that question had obtained a total of 5 - 1 = 4 votes, for a total of 50 - 2 = 48 reputation points. Strangely, the removal of the question from Main didn't cost its author these reputation points, despite the fact that votes on Meta are not equivalent to votes on Main (the former do not alter reputation). The fact that the question got migrated indicates that it was not fit for Main, therefore I was expecting the reputation points that it had brought to vanish after migration. Is this a bug of the SE software?
The question still exists on the main site, so they keep their reputation – for now that is.
The question is left as a stub, or pathway to the new site, for 30 days, after which it is automatically deleted by a weekly script.
(source: What is migration and how does it work?)
In a month or so, the question will be deleted from the main site, and then the author will lose their reputation.