Hi @esciencepress,
This is a tough one – I’m afraid you’ve run your database through a blender, several times, without a backup. I can’t walk you through correcting this in detail; we do clearly recommend that you make a backup before upgrading. If there’s any way you can recover using a known-good backup, I would strongly recommend going that route. Failing that, I would start with the earliest copy of the corrupted database you have, e.g. after the first failure happened, before you tried again. The more uncertain steps the database has gone through, the tougher it will be to clean up.
If that’s not possible, the steps that an upgrade goes through are listed in dbscripts/xml/upgrade.xml. You could try to ascertain how far your upgrade got by looking through those steps to see which were executed and which were not. You may need to run through these by hand, but be warned, they are extensive.
Regards,
Alec Smecher
Public Knowledge Project Team