There's no telling. I changed the price yesterday on all retailers. iTunes and Kobo already have it listed at 2.99. I would not say Barnes and Noble is "holding out," more like they seem to operate on a skeleton crew at all times (which makes sense given their financial troubles) and it takes far, far longer for them to update any changes.
Because of Amazon's pricematching policy, as long as Barnes and Noble drags their feet on changing the price, Amazon will have to meet that price on their own website.
I understood that this would happen when I decided to make Doc 0.99 at launch. It was more important to me to make sure that with the release of the Box Set at 9.99 that no long-time readers felt like they were getting screwed.