So, clearly the immediate danger is gone, or I'd have hoped that you'd have stayed in town! (Unless of course your sister when with you.

)
I think in this day of "CSI" and "Law & Order" and all the other procedurals out there, people think, "oh ... of course the cameras will have security tapes and of course there's a crew available to dust for prints". But this isn't TV and the cops have more than one case at a time and limited resources. If your sister is fine sleeping in the house with her son and having the locks changed and not continuing to be freaked out, then the cops are going to hang onto the file should their be a second contact, and move on to other things. There are lots of theories as to what the cellphone owner might have been doing there, but no immediate threat (only supposed ones). And the police can't act on what someone thinks might possibly happen.
Then again, he knows he's the prime suspect, based on the visit from the police. Even if he did call, no one would think that he's sincere. They'd all figure that he's calling because he's got some motive or he's trying to fake being concerned or whatever. When you're in that situation, pretty much any lawyer on the planet will tell you to just shut up and lay low. Don't do anything that might in any way be perceived as confrontational. Besides, doesn't the ex have a restraining order out on him? Does that even
allow him to make a phone call? I'm thinking no.
Unfortunately even an officer who KNOWS the ex was lying (but has no proof) won't stand up in court. Or, well ... anywhere.
Again ... if you were okay with going out of town for the weekend and leaving her there, then it's clearly "safe enough." Even if she was along on your out-of-town trip, she apparently doesn't feel anxious enough to move. I'm sure she'll be more aware of her surroundings and what's locked and what's not and so forth. But it does seem like the house is simply too large for her (if she never ever goes upstairs). Might be the time to downsize.