I've noticed a number of times where the available items for sale at an item merchant disappear. It's hard to find a consistent pattern, but two things that seem to be strongly associated:
*Loading a save game, esp. if no city is founded/no purchases have been made yet.
*Researching new items that are available for purchase
In both of these cases sometimes (although not always, seemingly) the old items disappear and can no longer be purchased.