Server ID versus license is really apples-and-oranges. If you haven’t provided a license that corresponds to the edition (and LOC, and server id, and…) you’re running then you won’t be able to perform new analyses. So yes, you need to obtain the new license before your upgrade. Regarding your server id, it’s held in your database so this part should be seamless, otherwise you wouldn’t be able to upgrade from version to version within an edition (it really is the same procedure ). But if you have any further concerns in this matter you should definitely talk to the contact who gave you the evaluation license for Enterprise Edition.
Regarding the Quality Profiles, what updates were you expecting? If your edition upgrade included analyzer upgrades, then you would likely have seen changes to the relevant Sonar way profiles, but that’s it, and an edition upgrade without a version upgrade is not going to include analyzer upgrades without further, manual intervention on your part.