I don't actually know the answer to your question, because you don't need to know (you just need to know one side has 12H20 and the other 6H20), but I should imagine the water might actually be due to the condensation reactions that occur when the molecules of PGAL are combined to form glucose after the Calvin cycle.
Glucose actually isn't the immediate product of the C-cycle, so if you're talking about building up a glucose molecule from its parts (PGAL, the basic product of the C cycle) water would be released when glycosidic links form. So I don't think oxygen is, at any point, combining with the H ions to make water, I think that's more a product of a surmised reaction which has been added to the simplified one you're required to memorise.
But I'm actually not entirely sure, haha.
Actually, addressing the first part of what you said those hydrogen ions aren't used in later parts of photosynthetic reactions. The H ions are actually used to create a concentration gradient so that ATP can be produced in the light dependent stages of photosynthesis. That's the ATP which is consumed during the C cycle (so no net production of ATP is in the equation, but it is produced). When water is split in the light dependent stages of photosynthesis the oxygen from the original six water molecules on the left side of the equation is released into the atmosphere, and the hydrogens participate in processes you don't need to know about for Unit 3/4. So the water molecules on the right side of the equation would have to form from different ions present in the cell. And this is why we don't just cancel out the six H2O on the left side of the equation and have 6 H2O on the right - we keep 6 and then 12 because they're actually different water molecules which are involved in different processes and the later water molecules are the result of different reactions than those which you might think occur looking at the 'overall' reaction.
THAT SAID, YOU REALLY DON'T NEED TO KNOW. BUT SINCE YOU ASKED!