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 :-)