In DocuWare 6 the configured Import Folders for DocuWare Import are stored in a file named "hotfolders.xml". This file is stored in a user-specific folder. This means if you change the DocuWare Desktop Service user, the jobs are no longer available.
In order to get the jobs back, do following steps:
  1. Change the DocuWare Desktop service user
  2. Move the files:
    • systemconfig.xml (general settings file)
    • all <WINDOWS-SID>.xml (connection files for Windows users)
    • hotfolders.xml (Import-Folder settings file)
  • from
    • Windows Vista, 7 and 8: 
      x64 Systems: C:\Windows\SysWOW64\config\systemprofile\AppData\Local\DocuWare\Desktop 
      x86 Systems: C:\Windows\System32\config\systemprofile\AppData\Local\DocuWare\Desktop
    • Windows XP:
      C:\Documents and Settings\LocalService\Local Settings\Application Data\DocuWare\Desktop
  • To 
    • %LocalAppData%\DocuWare\Desktop\ of the specified service user.
Please note that you can't share the files for every Client. Every Windows-SID is unique, so you have to do this locally!