I know here in the USA there were 2 clients being used for the BETA.

Phase 1 was the Beta Client.

When phase 2 became available instructions were to DELETE phase 1 Client from your PS4.

Install the Phase 2 Beta client > which became > the retail version once early access weekend became open.

Options were available to register your Phase 2 client > Upgrade PS3 / PS4 for Free.
you had to follow instructions to make this work.

I'm not from EU so.. i have not idea what structure was put in place to upgrade your PS3 to PS4 but i do know that it will not work if you didn't register you PS4 account on the MOG stations via. the PS3 / PS4 transfer. Check you MOG Station SE account.