A question that is off topic and needs to be migrated still needs to be migrated even when there is a bounty on it.
Currently, if you attempt to migrate a question from the flag queue, if the question has a bounty on it, you must
- open the question in a new tab
- clear the bounty
- migrate the question
- close the tab
- remove the flag from the queue or ignore it
I have never encountered a situation where I saw that an off-topic question shouldn't be migrated for the sole reason that it has a bounty on it.
If a moderator attempts to migrate a question, any bounties on that question should be automatically removed.