Srtiels once gave me the advice of clipping Cupids nails because when he mounted Aero she screamed ( in a video I posted) so you may try that as well and see if its his nails that are hurting her.
Honestly( and someone can correct me if Im wrong) though I dont think there is anything you can do about it other than wait and see if they figure it out eventually. My female does the same thing, she asks to mate but when my male mounts her, she flies away and wont let him do it ( but she also tries to mount my male so shes wierd
), and this has been going on for quite a while and they act like a bonded pair.
If they arent allowing one another inside the nestbox they might not be as bonded as you thought...do they follow eachother around? Preen eachother? sleep side by side? eat out of the same bowl together? (these are all signs of being bonded) Even if they have been together a long time and are mating it doesnt mean they are a bonded pair.
Personally I would remove the nestbox until they figure out how to mate properly, a nestbox encourages laying but if they arent mating then the eggs will be infertile.