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I don't know the ph level of the condensate. It should have no effect on making the drain sour. Maybe, the funk was in the trap, and when that water was draining into the floor drain, you had the sour smell residue but that is a long shot. Does that room smell sour? Bottom line is that you don't want to be drawing anything from the floor drain, so you should make sure both the coil condensate run & furnace run to the floor drain are trapped in one way or another. Also, I would make sure that all duct connections are sealed with mastik or mastik tape since the drain is so close.
If the drain does not have a sour smell, I would think the source of the funk has to be from somewhere else. I hope someone else has a better idea.
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