This poster at JREF mirrors my own thoughts and fears:
I must say that I'm very worried. The defense can not afford to let the other prosecution "evidence" go unchallenged. When it's time for them to give their closing arguments, the defense must stress the counter explanations for the "bloody footprints", "bathmat footprint", "mixed-blood", etc. I hope they don't spend the majority of their time debunking the DNA evidence because at this point that would be like beating a dead horse. A lot of focus should be on Rudy Guede and the evidence against him (especially his history as a cat burglar) because that is paramount in establishing the most plausible scenario of what happened that night. The similarity between his burglary of that lawyer's office and the break-in through Filomena's window needs to be emphasized.
The "mixed-DNA" issue I am especially worried about. While the last judge correctly disregarded the idea that the samples in question were of "mixed blood", he erroneously concluded that because they were mixed, they must have been deposited at the same time -- implicating Amanda. There are scientific studies that refute this notion, but is the new judge even aware of this? How about the defense team?
http://forums.randi.org/showthread.php?t=215085&page=160