I can only guess, if they wanted to throw in a few twists for the sake of the plot they could have some flood spores that survived Sharpened Shield's destruction (I know, no very original ala Aliens) that could have latched onto the SOF's hull or even worse- over the long voyage back home managed to take over the ship, corrupt Serina and consume most if not all of the dormant crew.
Come to think of it, dosen't the SOF's general sublight heading violate the Cole Protocol if they ever crossed paths the other covenant ships they would be unable to escape on a random vector so if serina managed to erase all sensitve info and herself wouldnt that leave the crew at the mercy of any would be aggressors?
I dont think the flood would have came abored, if anything could have, perhaps a group of spec ops sangheli made it. Then murdered everyone in there sleep. Not a cheery idea, but possible.