If they are using backups on their simulators/computers, they just restart from the last backup. Therefore if the root universe is using backups and all simulated are copy from the root, the system is stable.
The restart is not visible inside the simulated universe.
If we are in simulated universe, you don’t have to worry. With high probability (99%) the outer universe is also simulation.
Matrioshka universe is not stable because glitch on any level will terminate downlevel
If they are using backups on their simulators/computers, they just restart from the last backup. Therefore if the root universe is using backups and all simulated are copy from the root, the system is stable. The restart is not visible inside the simulated universe.