I am new to DNN but not to CMSs. In other CMSs with client maintained data I have too often heard the "it disappeared" story. I have spent so much time hunting witches I won't even go into it. Hearing this and seeing your advice about the log, is there a way to turn on a higher level of logging that more closely monitors user activities on the site?
A somewhat out of the box idea on this one... If the files can be verified to be publicly accessible (by accessing them in a web browser from a computer outside the local network), an external monitor could be used to check the availability of any web page. The monitor could then give you an idea of when the file disappeared. It's not perfect as you will have some delay, and there is no way to really monitor what happened to the file with an external monitor. What is more important than when, but sometimes when gets you closer to what.