Is the ruling of mosques applicable to a madrasa/mosque in a Chawl being redeveloped?

My question is a trust registered with charity commissioner as Powai Educational Trust took land on lease from landlord in Chawl and made an agreement with landlord saying they will use this as madrasa and will not built or use it as mosque. But now they are using that Chawl room as mosque. They perform namaz and also use it as a school. Now in this situation does the ruling of mosques will be applied on this place? As the whole Chawl property is going to be redeveloped. And for that the whole Chawl structures had to be demolished including this madrasa/mosque. Please guide.