ChirpStack Gateway OS uses an OverlayFS on top of the read-only root filesystem. This means you can make modifications that are persisted even after a software update as these changes are written to a different data partition.
Before performing a backup or upgrade, please make sure that the directories / files are listed in the files that must be included during a sysupgrade. This list can be configured in the web-interface by clicking the System, then Backup / Flash Firmware in the left menu and then clicking the Configuration tab.
To perform a factory reset using the web-interface, click System, then Backup / Flash Firmware in the left menu. Then click Perform reset.