***quod** facta sunt,* in eō *manent* = **what** they [= entities] have been made (as/into), they remain *in that state/as that thing.* The singular is needed because *quae facta sunt* (as in the first clause) means ‘the entities that have been made’, so that the pronoun is no longer a subject complement (‘made as/into something’), but the subject itself.

Parallel to this is *quantum accēpērunt, manent,* which is supposed to be ***in eō** quantum accēpērunt manent* 'what amount of substance entities receive, they remain with that amount of substance,' i.e. the law of conservation of mass :-)