I posted about this very problem about 10 months ago after we experienced broken file link issues multiple times (affecting several thousand links).  Each time this issue occurred our files were untouched but large groups of DNN file IDs were no longer valid.  Fortunately we were able to determine what was ultimately causing the issue as well as the solution (disable autosync as previously mentioned).

My posting below outlines the issue, its specific affect on DNN and why DNN's autosync option may need to be disabled (and also why autosync is not actually at fault, at least in our scenario).

DNN Blog - Corrupted Document Links:  http://www.eguanasolutions.com/DNN_Blog/EntryID/1.aspx

-mamlin