We’re only support upgrade function.
If you want to downgrade the JetPack, please using SDKmanager to flash.
You can reference detail from: Jetson Download Center | NVIDIA Developer
You should probably post under the specific type of Jetson, but yes, if it is an eMMC model, then this is replaced. However, you can make a clone of the rootfs for later use (a clone can be used with loopback mount to see or modify what is on the clone, e.g., a home directory). Instructions differ based on model.