More things I figured out.
Do not run:
notifications/upgrade-4.6.1-4.6.2
acs-content-repository/upgrade-4.6.1-4.6.2
etp/upgrade-1.1d-1.2
bug-tracker/(all upgrade.sql). Run them manually after the upgrade. Make sure to use the same user that is the owner of the site.
file-storage/upgrade-4.6.1-4.6.2
It seems that the site is already running on 4.6.2 though noone told the packages this :).
Furthermore, it is wise to run all SQL scripts for forums starting with the second and doing the first one last. I actually added the other upgrade scripts manually to the first one, so it (hopefully) speeds up a little bit.