There are others here who are much more knowlegable than I about breeding, but I understand it is best to wait until female is at least a year old for that. Do not think it would kill her, but it is better if she is completely mature, to reduce risk of any complications. I would definitely separate the two ASAP. Beardies should not be housed together after the hatchling stage, regardless of gender. Males fight each other violently, and dominate females, two females often have one who dominates the other, leading to poor nutrition,-the weaker one eats less, has less access to the best light/heat positions, and leads to overal stress, which makes them more prone to illness. Even if they appear to be getting along, owners have discovered that bulling takes place when they are not around, or at night. Since it is possible that your girl is now gravid, she should have a set up of her own that includes a good place to dig a hole for her clutch, like an egg box; if they cannot find an acceptible place, they can withhold the eggs and become eggbound, which is a dangerous, painful and sometimes fatal situation. There are threads here that specifically discuss the needs of a gravid female--time to read up, and take action!
Anyone else who has some breeding experience and has more/better advice for our worried friend?