We have 3 graphic designers using InDesign on Mac. Sometimes when saving an InDesign file, several links go missing and have to be readded.
All the files are stored on a Windows Server, and aren't being touched other than with InDesign. There is also no correlation with the missing links; it can be all the links in the file one time you open it, or only a few missing the next time.. This is not permissions based either, as every account has full access to the Server.