This sounds like file corruption. You will need to blank the department file and import the details again. When you add an extension or user, the department file is updated. There is not a separate configuration for departments.
The steps you follow to re-create the department file will depend on if you use extensions or pin codes:
- Extensions:
How do I import extensions from a file into TNG? - Pin Codes/Users:
Not all my users are listed - please add user on call list