I am not sure why your chain of command would tell you that your case would remain open for 5 years. I know of no reason that this would occur and do not believe it is possible if the case was closed favorably. Perhaps they were simply referring to the titling process. Here is an explanation of the titling process.
C.I.D. will not leave the investigation open for five years. If this was the case, the Soldier would have to be flagged and would not be able to reenlist.
What they may be talking about is C.I.D. probably “Titled” the Soldier during their investigation. This means that they named the Soldier as a suspect on a Report of Investigation (ROI).
If the Soldier was titled, it will follow this Soldier for the rest of his life. From what I understand, you do not get removed from this database once in it. So, anytime he applies for a government job, police, security, basically any job where they do a background check, this issue will come up.
I found the following recent article which explains the basics of the titling process.