I have just discussed this with our dev team lead and we do trigger a procedure that rebuilds indexes in our database. These indexes boost the report generation performance, as well as other database queries. If database is large enough, this process can indeed take some time.
What I suggest you to do here is to check whether the process is still running or not. By now, it should have finished the required maintenance preparations required by the setup and you should be able to proceed with the upgrade.
P.S. for other users, we will create a KB article, that would show how to rebuild indexes prior the upgrade, so that this process does not take much time.