Well, it was obvious from the lack of substantial information in the initial affidavits and the absence of follow up warrants that they have little evidence in the case.
Maybe LE got everything they needed during the first searches and follow up warrants were not necessary. If you do things right the first time, you don't have to go back and do them again.
They probably don't know much more other than she is dead and it was most likely a homicide. Finding HD's body is important since it eliminates possibilities, but I doubt they found much more in the way of evidence at the scene other than her bones.
It could go either way. There may have been a "stash" of evidence, clothing, coveralls, shoes, bed linens, a mask...who knows? Because LE isn't telling.
The big problem they are going to face after all this time is that there isn't going to be any physical evidence left if it hasn't been found by now, and any witness evidence is going to be hopelessly contaminated after over two years of relatively intense local interest.
I don't know that the initial witness evidence, while it was still fresh, was all that credible when it was only a few days old. Who knows what turned up in the county landfills, that has been preserved for evidence?
That is going to make the investigation an uphill struggle. Of course, they could allways go for a Hail Mary pass, charge SA and try to convict him on circumstantial stuff and emotion. I am not a big fan of that strategy, since IMO it produces a significant number of false convictions.
I think they will have a hard time establishing opportunity (or motive for that matter), plus there is the inconvenient problem in that they have a duty to prove beyond reasonable doubt while the defence only has to establish reasonable doubt.