I've answered a few questions now relating to this incident but the answer to the specific question you are asking is found in the court complaint
and the discovery material, which experts here cannot see. Without having access to the file or the court papers, all anyone can tell you is that the state is bringing the charges in the neighboring county because they have more or stronger evidence there than they do where the store is.
This is not unusual, since the goods left the store as part of the alleged act. Your son's lawyer should be able to tell you specifically why the other county has the right to prosecute your son, because he can see the court papers. If the other county has no relationship to the crime then the court has no jurisdiction over the case and the case should be dismissed. If the case has a relationship to the county, then it can be prosecuted there.
Can the state also refile the original case in the original county? Maybe. There is no way of telling without looking at what was filed with the first case, what was said on the record when it was withdrawn and what would be filed again, if it ever is.
Your son's lawyer is experienced. He should know how to resolve problems if they arise. If he thinks your son has a good judge and has worked in front of him before and they like and respect each other professionally, that can be very helpful to your son. Similarly, if he can get along with the DA.