They do restock!!!!
Sunday night I went to Once Upon A Toy and they had nothing Temple of Doom related which I figured would happen.
Wednesday I was at Hollywood Studios and the Stunt Show was closed (one of the performers passed away after a accident at rehearsal, so I'm assuming the show and stage was being investigated and whatnot) There was a kiosk located just a bit down from the show entrance (if you're passing the show on your right hand side keep walking down) and there I found Willie and a Temple Guard. Then if you keep walking down near the show exit there's an entire Indy giftshop where I found one lone TOD Indy and bought it.
Today before we left, we went to downtown disney once again and the store restocked on the TOD wave but there was literally one case. I don't know what the breakdown is, but all I found was 1x Mola, Indy, Shorty, Temple Guard and Willie. I left with Shorty. I don't know what days they stock, it could've been any day between that span but they are restocking...I didn't see any Mutts there though with the cycle