Can anyone let me know which one is the master PGO file in qv?
one is present in Qlikview Server folder and other is in Root Folder.
If i delete QVS folder PGO, will there be any discrepancy?
If you have yet the pgo-files from the root-folder you could copy them into the server-folder otherwise all related settings within the qmc must be new entered.
I'm not absolutely sure but I believe they are just copies of eachother. I think you should give it a try - if it's not worked or it seemed strange in any way you could reverse it again and you should stop the server for it and restart them after the copy-job.