بسم الله الرحمن الرحيم
In principle a land dedicated formally for salah is mosque from the earth to the sky; hence the ruling of second jamah in lower floor shall be applied to the second jamah in the second floor i.e. it is makrooh.
Note: You may offer second jamah in the outer portion of the mosque.
Allah knows Best!
Darul Uloom Deoband