The only way I know to do this is to edit the Category.xml file that is located at "C:\ProgramData\QlikTech\ManagementService\QVPR".
NOTE: If you do this make a backup first.
Stop all the QlikView services:
In the Category.xml file at the bottom you will see the Category names.
So, if I wanted to clear test2 I would delete the line below.
<Category Name="Default" ID="2472223c-a88c-4325-8ee4-89e6add69c9f" ModifiedByUser="system" ModifiedTime="2013-01-09T17:27:14.2535561-05:00" />
<Category Name="test1" ID="b871db88-9f53-477b-a7e4-a1c44f30f350" ModifiedByUser="QV-11-SERVER\Administrator" ModifiedTime="2013-01-09T17:37:57.6142861-05:00" />
<Category Name="test2" ID="d5187273-7fe0-4a9d-84a4-cadbbddaed4c" ModifiedByUser="QV-11-SERVER\Administrator" ModifiedTime="2013-01-09T17:42:03.2367175-05:00" />2
Thanks Bill. I had the similar problem and I fixed it by modifying the Category.xml file in C:\Documents and Settings\All Users\Application Data\QlikTech\ManagementService\QVPR. I am using Windows server 2003 R2 and using Qlikiew Server without Publisher in our test environment. The following is what I did,
1. Find the the Category.xml file in the folder mentioned above and make a backup copy.
2. Open the XML file using Notepad deleted the lines including <Category Name=" xxxx", xxxx is the category to be deleted
3. Save the modified XML file
4. Restart "Qlikview Management Service"