I believe the convening authority can reject the Article 32 investigating officer’s recommendation and have it done again. Since I wasn’t a JAG on active duty I’m not sure of that but as deputy to a convening authority I recall something like that. If he has the authority to do so I’d bet it’s rarely used, so a negative Art. 32 report will probably end that case.
That is my understanding from reading posts on other threads from legal officers but as you noted it is rare.