Did you follow all the Installation Instructions? Were there any errors during the upgrade?

Hi,

I have checked very carefully all the missing file and concluded that all the files is exist in Data folder but whenever I open those files / download from website, blank file is getting downloaded.

I am not sure what to do about this issues? Any help?

there is not such issues with new file upload.

Have you really done ALL STEPS of the upgrade instructions? Are there any system messages when you go to the admin section of your site about pending upgrades (you can also check the "Configure - Upgrades" section in the admin area). There is an upgrade that re-organizes the data directory that you need to start manually (also an update to convert comment database entries). If you haven't done these upgrades then it's very likely that any uploaded files are unaccessible and also any existing comments wouldn't show up currently on your site.