Rep loss related to downvotes on bad questions is refunded. But not until
- the question is deleted and
- a recalc happens.
Now, global recalcs actually did happen in the misty depths of time, but not recently, so the second condition is only fulfilled if your account gets a recalc for some reason. You can request one, but it is often not a great idea (you may lose more then you gain).
A side effect of this is that you shouldn't downvote every question that needs closing. Those that should be migrated and those duplicates that have sufficiently distinct titles to be worth keep around for search reasons will not be deleted, and the rep will never be refunded.
It is probably best just to stick with leaving a comment.