There's no reason why you can't do that. I would definitely keep the first "half batch" simmering until you can add the second half batch to it. That way it won't get infected with some nasties. But if you combine the half batches, chill it , and pitch the yeast, it should be pretty much the same as doing a full wort boil.
After a year of sitting idle, Andre's All-Grain Brewery has reopened.
Batch #59-Kolsch (Secondary)
Batch #60-Blueberry Ale (Primary)