It's impossible for me to comment on whether he was innocent or guilty of his charges. That's the job of the jury who heard his case.
A prosecutor does not have to explain why he has decided to nolle prosequi a case. A nolle prosequi simply means that even though charges have been filed and prosecution of the case has begun, the prosecutor does not want to continue prosecuting it at that time. Typically, it means that the prosecutor does not have enough evidence *at that time* to continue prosecuting the case. And, after doing a nolle prosequi, the prosecutor has the option of refiling the charges.
Keep in mind that prosecutors, as well as law enforcement officers, have a great deal of discretion in deciding whether to make an arrest, whether to file charges, and even whether to continue with prosecution of a particular case after charges have been filed -- that is, the prosecutor has the discretion to nolle prosequi a case and refile it at a later date, or, forget about it altogether. Not all of their actions can explained or understood, because again, they have a lot of discretion.
So, if and when the prosecutor does choose to refile a case that has been nolled, t may very well be assigned a new case number. The case number XXXXX XXXXX an administrative detail that really has no bearing on the case itself - it's merely a way for the court to keep track of the case.
Hope this helps.