Hi there, welcome
Unfortunately this is a common problem, and it’s great that you’ve already separated them. Unlike some other animals, bunnies don’t tend to remember family relationships once they hit puberty and get hormonal.
If you want to eventually have them live together again, you will need to get them spayed, and then go through the bonding process with them once they are healed. This involves supervised sessions in a neutral territory to allow them to safely sort out their dominance hierarchy. If you check out the Bonding section under the bunny-info tab at the top it will give you the basics.
Spaying should also help with their territorial and aggressive behaviors, and will prevent them from getting reproductive cancer (which is very common in unspayed female bunnies).
In the meantime, make sure they cannot access each other, even though cage bars, as any nipping or squabbling can make it harder to bond in the future.
To improve the temporary housing situation, my go-to during bonding has always been NIC cube condo cages, as they can be disassembled easily and re-purposed once they are bonded. This link has a basic plan that would be great: http://www.bunssb.org/bunnies/perfect-cheap-bunny-cage/.
You might eventually want to get a couple x-pens to divide up their free-roam space with a buffer, so they can’t nip each other during play time.
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.