I had a similar problem a few weeks back. The book was coded as "-1¢" instead of $0 and in the payment routine it must have hung up: a credit card can't be charged "-1¢" so it got confused. By the time ti was sorted out, the free book was converted to paid. Customer service -- at their prompting, not mine -- offered me another free book of my choice from a designated list (I used the code on something not on the list ...).
My experience with Kobo service has been really good. Why not write back to the person who first responded and explain the book has now gone to "paid" status? I will bet they'll find a solution which works for you under the circumstances.
Once you have firm resolution, would you mind replying back here?