Such separations are often difficult for children and your daughter's regression is understandable. Can the impact be overcome? Yes. You are doing what you can to provide the girls with a stable home environment while you are away, and that is all you can reasonably do. It goes without saying that it would be better for your daughters if they did not have to endure these separations, but such developments have always occurred with military families and there's no reason to think that the girls will not develop well.
Since you have been in the military for 12 years I am sure you have more then servered your required time on active duty. Is there any way you could get a job stateside and maybe even a permament job at a military or AFB? This way you could continue your career and still be with your kids.
While I am not a doctor I wouldn't worry too much about a 3 year old being braty at certain times as this can be a tough age for a lot of kids.