You can certainly touch it up using cold blue. It usually blends right it and looks great, the problem is it wears off if you keep touching it. Because of the nature of a bolt rifle, it will wear off after just a few hundred rounds.
That is really annoying. If they are paying for the shipping, I'd just ship it and have it taken care of. Then you will be happy and hopefully its all well and good.
There is no such thing as a stupid question, only stupid people.