For example:- Have you repaired the machinery?- Yes, I have repaired (it / them).
I would always use it. The word machinery is singular.
It is a word like furniture, equipment, information, etc. no plural form exists as they are non-count noun, so IT is the pronoun to use.
It depends on how you are using machinery. If you are referring to the works inside a single unit: I repaired it. If you are referring to an entire floor of machines that needed attention: I repaired them.
