Do you mean that the actual jar file is being removed? Or is it disappearing from the Investigator only?
APM does not physically delete any management module, so if that is the case, then it is an external source that is deleting it. Possibly another colleague not realizing its needed, or if its the same one frequently, could be an antivirus flagging it wrong for some unknown reason.
If its only disappearing from the Investigator and not physically from the disk, sounds like some sort of memory issue. What is the Xms and Xmx in the EM and the amount of RAM on the server? Are you using Webview as well?