Moderators can cancel and thereby refund a bounty (only to be done under special circumstances). If you flag and ask for migration they might agree to first cancel the bounty and then migrate it.
As mentioned in a comment a question with a bounty cannot be closed (and thus also not migrated); this restriction also is present for moderators.
As sources see for the cancel mechanism How can we close questions with bounties? and also as part of the MSE FAQ How does the bounty system work?
