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Association between a long name and a particular short name may be lost:
  Older repair utilities will delete long name - invalid directory entry.

  Copying to another directory, if short name already in use.

  Opening and saving files with app. that only recognizes short names.

  When using Backup utilities not designed for VFAT. Win9x comes with a 
  utility called lfnbk.exe (on cd) that will backup the short/long 
  association in a text file and deletes the long names.  lfnbk.exe can
  then restore names to a restored directory structure. 

  Backup software may cause the short alias name to be associated with a 
  different long name when restoring.
    If restore is done in directory with existing files.
    
    If two files with the same initial characters in long name are restored
    in a different order than created.

    myprojectmondy -  mypro~01   myprojecttuesday - mypro~02

    If restore restores second file 1st, it may be mypro~01