I posted a slightly off-topic post in Super User, got downvoted, then admin migrated my post to Stack Overflow, although the downvote has been cleared, but my deducted reputation wasn't restored. is this normal?
It is normal. The original question (now a migration stub) is still here.
While the question exists here it has a downvote on it. That downvote counts. Downvotes on questions do not get migrated, but they do get left behind.
If the question is deleted on this site then it should reverse the downvote, but we don't immediately delete migrated questions so that the history can be seen. The roomba clears up these migration stubs after a while as well, another reason why we don't worry too much about clearing up in this case.
It's only one downvote though.