RROP states 'once substantial action occurs a misdeal cannot be called', even where the (self) dealer has lifted the stub, and muck and commenced shuffling, the hand still has to play out and the deck has to be reconstructed in as fair a way as possible.
Given that the muck is now mixed with the stub I would say that there is little point in trying to pull out the issued cards and there is no way you can correct the board cards to ensure they will be correct so shuffling the deck and issuing a flop as if playing heads up seems to be the only way to proceed in this situation. Another urban mith, that of calling a misdeal, always remember once action occurs, the hands HAS to play out in someway, shape or form, in the fairest way possible.
Now say for example the dealer scoops up the board post flop (once the flop is issued), and shuffles the board cards along with the muck and stub together, not realising the hand has not finished. In this circumstance you would have to try and reconstitute the deck and board, you probably aint gonna get it right and people won't remember what they had, but you can't know that stuff anyway because the hands still playing so best to keep those cards in with the floor staff taking out the cards that formed the flop and then reshuffle to issue to remaining streets.
As for Chet's suggestion of suspending betting during the hand, I would be in support of that, BUT here's the thing that happened at one of my self deals:
heads up to a raised flop,
button deals, issues flop (in hand) UTG checks and button (dealer) announces all-in, UTG says call, but button scoops up his cards, stub, board and muck into one pile - he's finished in the tournament because he had less chips, but that was easier as he fouled his hand first, so his hand was dead, unlucky but shows the reasoning, and similar reasoning should be applied in this circumstance.
Regards
Stuart