David Uploaded His Programming into Walter

David Uploaded His Programming into Walter...

You will recall that Daniels stabs David in the chin with the nail pendant that she wears.  Note that the android that is aboard the ship at the end of the movie bears no such scar, indicating that the android chassis is that of Walter.  However, it is clear that David's A.I. now resides in the chassis of Walter once they are back on board the Covenant.

David's programming was either uploaded into Walter, or Walter's programming was "rolled back" to that of David, in a similar way that you can roll back MS Windows to a prior state after a software upgrade.