Yes, I have two roosts at two different elevations. Plenty of space for two birds. And both are above the level of the nesting boxes so they don't sleep in there.
Just odd that they stopped roosting in there after a year of no issues.
The ONLY time we had a refusal to return to quarters was when a mamba rat snake was discovered in a hutch of a breeding pen. The Mottled Javas refused to re-enter the hutch for at least 3-4 weeks after the snake was removed from the equation. They were even laying their eggs in their dust bath area.Did you check for predators living in the coop? A snake can hide in a small spot.
So @Redhead Rae brought up a very possible scenario.