Please help with my beardies!!! :(?

I have a reptile shop and have been breeding beardies for 12 years. It is totally normal for a male beardie not to leave the female alone and it isnt the male who governs the females body clock, but her. If her body clock says so, she will lay, say 8, clutches a year, with or without the presence of a male, so keeping them seperate will not stop her laying. Another year she may not lay a single clutch, even though he mates with her. I always keep mine together, it gives them both their natural roles. In the wild they live in little harems of one male to several females. Yes he can sense her and if he sees her then he will make a "flying leap" to try and get to her. Arm waving is a sign of being subordinate which he was probably doing to you because you calmed him and then he spotted her and did the hierarchy bit by head bobbing. All perfectly normal. As she is digging, have you got your laying box in there for her and your incubator sorted? If not you really need to. Good luck