How would they have known anything about it, one way or the other, at the time they were searching? It's not like they interviewed all the Dealey Plaza witnesses first...
I've never heard of anybody suggesting that there was more than one gunman and one gun in the TSBD at the time of the Coup d e'tat. And the police had been lead to believe that there was a single gunman in the building because Howard Brennan told them he saw a LONE (single) gunman standing and aiming a hunting rifle out of a sixth floor window... Likewise Arnold Rowland told the cops that he'd seen a LONE man with a HUNTING rifle behind a sixth floor window and Amos Euins told them he saw a "pipe like thing" sticking out of a sixth floor window.
There isn't a single report of anybody seeing more than one gunman and one rifle in the TSBD at the time of the coup d e'tat. So there would have been no reason to search for another rifle after they found the Mannlicher Carcano....