Lack of compliance with medications can cause all sorts of complications. With him going off and on them like that, expect that it'll take a little while before he's stabilized again--assuming he keeps taking them this time.
If he's having problems with his meds, he should be speaking with his doctor rather than just discontinuing them--just dropping some meds can cause more than a relapse of symptoms. Not all meds are created equal, nor are their side effects, there may be meds he can take that won't produce the side effects that are bothering him (or at least maybe not as bad).
I have to ask, how much have you learned about schizophrenia? When in a relationship with someone who has it, it's to your advantage to know all you can about it. There are things you can do together that can help.
Keep an eye on that child as she grows, too.