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.
Although this gives the complete freedom to make modifications to the root filesystem, it also means that once you make a modification a ChirpStack Gateway OS update will never "overwrite" this changed file. In reality, a ChirpStack Gateway OS update will still update the file on the root filesystem, the OverlayFS will present you the file from the data partition.
To "rollback" changes, you can simply remove these from
Removing all the content from
/data/upperdir would effectively be a "factory reset".