When I first got Shiloh and Gizmo they were best buddies. Gizmo loved attention and Shiloh never bothered with me, but I tried anyways. After awhile they started doing the same thing. Gizmo would chase Shiloh and after very short bit Shiloh would bark at him.
Like you said, it wasn't a nightly thing and they got along great most of the time, so I decided to leave them together. Shiloh became even more withdrawn than before. Often he never left his wooden house. I got to watching them closer and it had become a nightly thing, Gizmo was even stopping Shiloh from eating at the same time as him.
Out of fear of blood shed, I choose to separate. I felt bad for a bit because they both seems so lonely, but Shiloh blossomed. Turns out, away from Gizmo, he is the sweetest little guy. Not much for being held, but loves pets and scratches. To this day, they both live alone.
I tried repairing both of them but Gizmo was to aggressive. Shiloh found himself a playtime buddy with Tucker, but got defensive and territorial once in a cage. So they were caged side by side and played together outside their cages.
I'm not saying the same thing will happen to your boys, just wanted to share my experience with it. If you end up having to separate maybe they'll be playtime buddies, but not cage mates.