No professional investigator or materials engineer would be confused by scrapes or scratches from the recovery effort.
As a professional aviation investigator and materials engineer I concur with peekay4's comment.
Moreover, I think it is important to not overplay the significance of the airframe impact damage. Think about what happens when an aircraft impacts land rather than water. Events X, Y and Z occur at altitude, leading to aircraft loss with ground impact. There will often be massive deformation, tearing and even burning of the airframe as a result of the ground impact. For the most part there is not a lot of significance that can be attributed to the somewhat random large-scale airframe damage caused by ground impact, other than determining things such as approximate speed, attitude and angle at impact (I'm in no way saying that impact damage and ground witness marks are unimportant, just that for the most part these are a consequence of a chain of preceding events that are often more significant to the investigation). Despite extensive ground impact damage, the evidence of what occurred is still there to be found, and far more often than not the factors leading up to the accident will be determined by the investigation team.
It is not easy hauling damaged airframes out of water without causing additional deformation and damage. My point is that some salvage-induced damage is not likely to be a big deal w.r.t. determining what happened with this flight.