We had a Qlik sense server 3.2 SR2 instance which we required to upgrade to the June 2017 version. I tried several times without success. I reviewed a lot of posts here but none of them described my situation therefore I tried almost most of the solutions related to upgarde problemas even if they were not describing my problem. This strategy helped me to learn a lot of tips, but it didn't solved my problem and then I decided to raise my problem to support.
I went to the support portal and I found this fix at the support Knowledge base that finally helped me with my upgrade. https://qliksupport.force.com/QS_CaseWizardKnowledgeArticle?id=kA5D00000004NPTKA2
For all these people that had a problem like mine I want to share my experience hoping that it might help somebody in the future.