Well, I didn't like to say anything...
Your explanation above sounds a bit overly complex actually, in that you're saying the validity of Massei's ruling is the issue, rather than the fact there was an acquittal and then a conviction. Obviously if there's something about Massei's ruling which the ECHR would consider a violation, that in itself could be enough for them to rule in favour of A & R, regardless of what went on afterwards. The main thing would be that the conviction was based on a flawed consideration of the evidence, not that there was an acquittal at some point.
The more I think about it, the more I think the DNA issue really is the crucial one - the statements from the SC and Nencini that the defence need to prove the way DNA might have been transferred or items contaminated (it isn't enough to show that the scene was handled poorly), and the refusal to hand over documentation. That principle, that the defence need to prove contamination, is why they were convicted, so it's absolutely decisive. I'm not sure how that would fit into an application to the ECHR, what particular violation could be claimed; it would be nice to think the SC might refer the case to the Joint Section to sort the issue out, but that seems unlikely.