While I understand your desire to have budgie chicks, given the circumstances it's simply best to interrupt this breeding attempt while it's still at the very beginning.
By placing your male budgie back in and continuing on with the breeding, you will be risking the very life of your female budgie (the level of aggression in a budgie can escalate quite fast and exponentially increase when in breeding condition and during the breeding journey).
It's not recommended to breed from budgies who have more of an aggressive temperament because not only the female but also the whole clutch would be at serious risk of being severely injured/killed. Temperament is also inheritable, so the chances for the chicks to get the father's aggressiveness would also be higher.
Even if you were to separate you male and let the female to carry on in laying a full clutch and incubation, the whole process would be compromised due to the lack of support from a good mate (in terms of feeding the female and making sure she is well care for while incubating) and the chances for the female to get too overwhelmed would be much higher and so would the chances for nest abandonment.
If one or more chicks were to hatch and would need to be saved by you due to parental neglect/abandonment/abuse, would you be able to hand feed and raise the chick(s)?
Do you have any previous experience in doing so?
Your female has gone through 2 full clutches previously which were all fruitless, it's not fair to let her go for another round given what has happened in the past and knowing the support of the male would be non-existent, not to mention the threat he poses to his mate and the eggs/chicks.
She would only be tiring herself and depleting her calcium reserves for nothing by laying a third full clutch.
Again, I will reiterate this because I firmly believe that for both of your budgies' welfare and safety, the best option is to end this breeding attempt and to simply give up on it, because they are not a good match and your male should never be on any future breeding plans.
Just because your male is sometimes loving towards his mate that doesn't mean he will not attack her or any eggs again.
Aggressive budgies can still mate with a given partner and the next day or hour can seriously injure the mate, it only takes a split second for tragedy to happen and by keeping your budgies together, you will be taking that risk.
Think carefully on this and make your decision by not placing your desires/personal expectations first. The general health, safety and happiness of a pet should always come first.
If you actually let your budgies to adjust to the changes after being separated, they will eventually calm down.
During the first couple of weeks you can even place your male's cage on a different room, close both doors and have some music on in each room they are in, so that any flock calling is muffled.
To help the budgies settle, you can also cover their cages on 3 sides. Dividing your time between them and taking the opportunity to reconnect with each of your budgies by spending one-on-one quality time with them will also do wonders.
In case you don't know, budgies do not respond positively to "punishment", nor this is something that would be effective in terms of correcting a bad behaviour.
The right way to proceed is by using positive reinforcement techniques that reward good behaviour: Using Positive Reinforcement in Training