Just checked the footage again from cricinfo, Pant does mark all stumps again.
Firstly, Smith scrubs off after shadow batting not before shadow batting. If one was really shadow batting, he would mark first then shadow bat, who would do the shadow batting first and then mark crease..
Secondly, marking in crease would be to mark a line, but Smith looks like he isn't marking a line but scrubbing out at multiple places as if to join/erase several markings
Third, Smith wasn't even shadow batting, he just comes, stands and takes a look, then rubs and leaves, so don't buy the the shadow batting coverup.
Lastly whether he was successful in erasing out marking or not is moot as he had only a couple seconds before batsmen got to crease so possible that whatever he attempted wasn't fully successful, the fact that something like that was even attempted itself is bad enough..