The separator should be fine, as long as they cannot reach one another through it. Like, if its just bars/grids, youll want to find a way to block it off. I have sheets of coroplast i used for something similar, but i think i have heard some people using fleece blankets. Be away if you use blankets to block them, youll want to wash it everyday, so make sure you have atleast two fleece blankets to alternate. Youll also want to make sure they cant climb or rip down the blanket
That sucks it wasnt actually waterproof! If you have the money for it, i always recommended people check out C&C cages for coroplast sheets and/or the coroplast cages. They even have half covered dividers that might work for you. For a custom divider, you can either use multiple of their single dividers and use clips to keep them together, or buy the grids and coroplast sheets separately and set it up however you want to. They are the cheapest ive found for their size, and my bunnies love their stuff!