I would guess from their popularity, HT will continue to stock them until [and maybe even after] the new run - that's assuming they can get new stock. They are hugely popular and HT and Funko will want to continue to meet demand. They may have some lulls in stock like any retailer who carries a product which is more successful than originally planned, while new product is actually manufactured - I would guess thats why they have vanished from the website.
You can find their old pages, perhaps if you get the HT product code from that and contact HT or go in to store they may be able to tell you for certain if your store will be getting it back in soon.