We've upgraded Qlik Sense from 3.1 SR1 to June 2017, but we "avoid" the steps were you are stuck (upgrade directly to June 2017), so we did this:
Upgrade Qlik Sense 3.1 SR1 to 3.1 SR2 (Sync Persistence)
Upgrade Qlik Sense 3.1 SR2 to June 2017 (Sync Persistence to Shared Persistence)
I think this steps for me are safer than doing it directly to last version.
I hope it helps.