There shouldn't be any data loss when updating Piwik. What exactly have you done? Did you use the auto update within Piwik or did you perform a manual update (uploading):

manual update

how exactly did you perform it? Did you remove and reupload all files, or simply uploaded and overwrite? Did you reuse the same config as before? Did you perform the (database) update on console?

no its totally different server..we have built complete PHP and MySQL server and then downloaded latest piwik.. and installed it in the server with latest version..

then why are you talking about an upgrade issue? You could have reused old data be importing the database before. if you already started tracking in the new database, there is no simple way to reimport the old data.