Hi Ondrej,
I've found a bug in the upgrade script. You have to exit upgrade.sh after the directorystructure pass and start it again to continue with the other passes.
That's what I use to do, to check that everythings all right, so I haven't discovered this bug before.
If you copy the wb_dmp files to $pwrp_db, and run upgrade.sh from the 'classvolumes' pass i hope it will work.
You don't have to remove any lines in the wb_dmp-file. You just have to notice which references are missing and correct them later in the database. My guess is that they were present already in the 4.6 version and has nothing to do with the upgrade itself.
/Claes