Well... you have a few options:
First, if you can ADB to the device, then drop into a shell and run the 'echo boot' command from there and verify with the 'cat' command that 'boot' is first.
Second, it would indeed be nice if NVFlash was that easy on our device (tf101) but it's not; we need --for a better lack of term-- a proxy, and that would be 'Wheelie' it was started by 'rayman' and you can read/get started
HERE (Linux) and
HERE (Windows)
Third, if you can make a full NANDroid backup, then you can always do a Selective/Advanced restore, e.g. /system or /data or both after a 'wipe/rebuild' of your device.
Fourth, backup your 'User' apps with TitaniumBackup and anything on 'Internal memory', e.g. Docs, Pics, etc...(you can use TWRP terminal and copy to external SDcard), in case you choose the third option and it fails.
HTH,
-JR-