Today I handled a flag on a question that was migrated to Engineering and subsequently closed as "unclear what you're asking," rejecting the migration.
I decided that I wanted to unlock the question. Since it had been deleted on its original site and was on topic for our site, I wanted to remove the migration notice as well as it was no longer useful. For reference, here's what a migration notice currently looks like:
migration rejected from unicornify.stackexchange.com Mon dd at hh:mm
This question came from our site for balpha's magnum opus. Votes, comments, and answers are locked due to the question being closed here, but it may be eligible for editing and reopening on the site where it originated.
Since the migration history is the direct cause of the lock and both are addressed in the banner, I did expect that clearing the migration history would also unlock the question. I did not expect, and was unpleasantly surprised to find, that clearing the migration history would also re-open the question (the "closed question" banner is separate). I wanted the question to stay closed so that the user who cast the flag could vote it into the reopen queue for the community to re-evaluate, as would be done with any non-migrated, closed question.
I understand that closing the question caused the migration to be rejected; this behavior changes closing/reopening from cause to effect, which I really don't like. When making decisions that affect how users can interact with content, we should be careful not to place too much importance on meta concerns like whether the question was migrated and where from.* A change to the migration history doesn't suddenly make a question clearer or more broad; it doesn't even necessarily have direct implications for the question's topicality.
More generally, I think this is a case of an action with too many side effects. I would suggest that, in principle, an option that says "do something" should generally just do that thing; sometimes two things is okay, but if it's doing three distinct things (from the user's perspective) it needs to be looked at.
The "clear migration history" mod action should not reopen questions. In the case that the migration history is cleared from a migrated, rejected question, we should still see that (up to) 5 members of the community voted to close the question. Instead, in order to get the desired result (question stays closed), the moderator has to close the question again after clearing the history, adding junk items to the revision history and removing the names of the (up to 5) community members who originally voted to close from the banner on the question.
If this proposal is rejected, at the very least I think it would be appropriate to rename this option in the mod menu to make the side effects clear, along the lines of:
* For example, I know at at least one case where placing too much importance on migration status spawned no fewer than four Meta discussions across three sites—see Meta HSM #1, Meta HSM #2, Meta History and MSE.