Maybe it is a good approach to first upgrade to Mendix 6.12. This version already shows a lot of deprecation warnings regarding a mendix 7 upgrade. The upgrade to mendix 7 will be much smoother if you first take care of everything the modeler shows you.
Best approach is like Andreas said to go to the latest version of Mx6 first. Also check the link provided by Mx:
As for the unique constraints setting to the database. After going to the latest version of 6 and than going to the 7 version you keep the unique constraints in the runtime. You add the migration toolkit(which you can request by support) module to your project and create a package with the unique constraints in the runtime and the migration toolkit added. After this you create a package without the migration module and with unique constraints in the database. After releasing the version with the toolkit on your TAP street you can run both the assocation migration and the Attribute migration. Hereby some printscreens provided by Mendix itself in there migration toolkit document:
You can resolve each conflict by double clicking on the item and updating one of the records. One tip, we've learned that every time you update a record the module triggers a refresh causing a total retrieve of all conflicts left. In case of a large database this takes a long time. So we manually deleted this refresh from the action behind resolving a conflict. To make sure you didn't forget one conflict we opened the page again to see if there are any conflicts left. After every conflict is resolved you can go ahead with releasing the version with unique constraints in the database.
I've did my fair share of upgrades to Mx7 yet, didn't run into issues so far. If you get errors of trying to create tables which already exists than I would contact support with this issue. But so far my experience is if you follow above steps from the Mx Unique constraints migration toolkit document you should be fine.
Thanks Tim, Corne and Andreas!
The problem we are facing is not with data-uniqueness but with mendix trying to create tables that already exist. As per your suggestion, I have created a support ticket for this issue.