No, flagging does not cost you Rep.
It looks to me like you were downvoted here and that's why you lost 2 rep.
EDIT: Wait, you flagged your own question to have it merged in with your new account. I see. Then you probably triggered a reputation recalc on yourself, either that or it was a byproduct of the merging. See:
Inconsistent Reputation After Merge
How do I know if my points have been recalc-ed?
How can I request a reputation recalc?
Also, I was given the relevant part of a sample merge log in chat:
Beginning merge into master User 'user4834' (Id=4834) for merge User 'user4890' (Id=4890).
. . .
Recalculating rep - before: 1
Recalculated rep for User.Id = 4834 -> old rep = 1, new rep = 1
As you can see, a rep recalc is triggered.