I have installed a linux file server and it works great. At my location we have a mix of Mac & Windows systems. Netatalk and Samba are setup on the server. The problem is recently someone has deleted file or files haven't been put on the server properly. Two different departments are pointing fingers blaming the other one.

Is there a script someplace that will keep logs of every file and how it's been added/delete/modified? I expect fairly large logs due to the amount of data that is changed daily on the server but I am confident I can parse through the logs fairly quickly. Or is there a second option that I am overlooking?

If the file is deleted through Samba, you can get detailed logs in the /var/log/samba if you have high debugging levels turned on. However, I don't remember much about Netatalk logs.