There are many partitions involved in booting. “APP” is the rootfs. Either of those commands would correctly restore the rootfs.
The command which says to restore “only” the rootfs is the “-k APP” (had you not used “-r” it would have generated a new image and overwritten your clone). Since you used “-r” all is ok.
All of those other partitions beyond “APP”, if they are from the same version the rootfs was from, will be fine. If the previous version was already from this version, then the other partitions are simply updated with exact copies of what they were already. A rootfs from one release to another will tend to fail because of boot setup not being compatible with the rootfs. This could happen if you had a clone of R27.1 and used it on a system where all of those other partitions were form R28.2. Either way though your rootfs should have been restored by this.
It does make me curious as to what went wrong with the error 13. Is your JetPack from the same install release version as what the rootfs was taken from?