You need to take a fresh sample of poop for them to test.Thank you very much for the advice, we will see when we can take her to the vet to get her and him tested. We're also planning to spay and/or neuter the male depending on what the vet suggests so that we don't end up with babies every year, we're already expecting our first clutch next year as they've already mated.
My male, Scooter, is actually smaller than our female, Phoenix, and he's a very timid little guy around her and around us. If anything she's the one who would bully him but she pretty much avoids him so I doubt we need to worry.
However, if I do notice signs of aggression besides him defending his food from her insatiable appetite I will seperate them. We already seperate them now during feeding times since we noticed that.
I've never heard of a tortoise being neutered - sounds pretty drastic and dangerous for him compared to the simplicity of just separating them. Maybe @Tom @Yvonne or @zovick will know more about that.