The Mender integration is a bit complicated on the TX2 when U-Boot is in the boot chain. Mender uses U-Boot variables to switch between the two rootfs partitions, and that’s a separate mechanism from the A/B slot mechanism in the NVIDIA bootloader chain. The tegra-specific Mender state scripts try to keep the two in sync and automatically re-sync them when possible, but there may still be some cases they don’t handle.
You might want to start a thread over on the Mender forum about this.