The phone pings they talk about in the affidavit are actually times for texts/phone calls, not pings. Presumably the ping data had been overwritten by the time LE went looking, so they only had call routing data available. There was no break in service, he simply didn't make any calls in that period (between the time he has in the vicinity of CC and when he was in BS), so they cant be sure if he was in one place or the other.
It doesn't really matter though, since there were multiple sightings of HD that day, when SA was clearly in Big Spring. Also, there was the text sent from the house cell phone to MB. Whoever sent it could not have been either SA or BD since they were in other towns at the time. It would have to have been someone who knew HD and knew that she was friends with MB, which limits it to HD, DD or CD, with HD being the most likely person. So, whatever SA did or didn't do the previous night or most of that day is irrelevant to the case. The time frame that needs to be examined would be from the period SA returned home and after that.
As I said, the time available for him to actually do anything is very small, so, the most likely scenario involves him arriving home unexpectely and HD taking off soon after that as a result. IMO HD had something that she was not supposed to be doing planned with local kids (or maybe someone else) that day at the house (which could be the meaning of the message she sent to MB), but when SA suddenly arrived home she had to take off at short notice to intercept them before they got to her place. That is why she gave the fake excuse for where she was going and why she left very soon after SA got there with little preparation. She didn't have time to get her stuff together, or choose clothes or anything like that, she had to act right away. Where ever she went after leaving home, I think something happened to her, possibly unanticipated, such as an accident, and it is being covered up.
I think there is also good reason to believe that she did in fact go to her fathers house sometime that day, allthought that probably has nothing to do with what happened to her either.
Whatever happened to her most likely happened that evening or that night. But unfortunately the clues for that period are completely lacking.