What is the ruling on two Friday prayers in one factory separated by a wall?

Friday prayer is not to be performed at the workplace, and the general rule is against multiple Friday prayers unless there is a legitimate شرعي excuse. As for congregational prayers, there is no harm in performing them multiple times at the workplace, and your prayers are valid, whether there is a partition or not. However, it is better for everyone to pray in one congregation, based on the saying of the Messenger of Allah, peace and blessings be upon him: "A man’s prayer with another man is purer than his prayer alone, and his prayer with two men is purer than his prayer with one man. And the more numerous they are, the more beloved it is to Allah, the Almighty and Exalted."