Not completely sure about your response here. So the CalData.pgo does exist under C:\ProgramData\QlikTech\QlikViewServer and is being modified continuously, meaning there is activity for it? Please confirm.
Are there users accessing the server that is using CALs? Can you try adding a few users and use a few CALs?
The CALDATA.pgo file in root directory is not reflecting the current changes. But CALDATA.PGO files under C:\ProgramData\QlikTech\QlikViewServer in each server is getting reflected till date. Is this causing the issue in converting the pgo into XML.
Just checked my own environment, and indeed it is created. It does contain information about all kinds of CALs (just tested Document and Named CALs). If you have Document CALs the .meta files will contain some of this information too.
Are you using Named CALs?
Try applying/removing the Server license again (note though that this will remove all CAL data), and you should see changes to the XML files, including CalData.pgo.