The act 2 mushroom might interfere with Nixfix recognizing that you have the quetzalcellona mushroom, but it should not have anything to do with it being there or not.
In the room to the far west of Nixfix, number 19 on
this map, there is a lever to get into the smaller room where you should find the quetzalcellona mushroom. As far as I recall, it should just be sitting on the ground.
Did you maybe pick that up while exploring, and think it was the act 2 mushroom when you noticed it later?
There is a way to get a replacement mushroom, but I will need to load one of my saves at that point to get the
inventory files.
EDIT
The topic above has been updated with these inventory files.
The mushroom is just called 'mushroom', and should be sitting in the north east corner of the room in plain view (
screenshot).