So now you have a couple of options.
Since the fry are free swimming, you can move them into the tank you have the female in and move the female back into the tank with the male. Rearrange the tank before putting her back in. With territorial fish, rearranging the tank causes them to lose the territory markers, so it's a "fresh start" This is if you want to keep the fry.
The other option is rearrange the tank and add her back in. Leaving the fry. Chances are good that the male will eat the fry, so this choice is if you don't want to keep them.