Did you have to upgrade to 4.21 first or some other intermediate version before the upgrade to 4.3.x?
What doc did you use? HP_Fortify_SSC_Install_and_Config_Guide_4.30 ?
I did it without any problem, on a 1 TB ORA DB. The only trick I did: I generated the migration sql, opened it in sqldeveloper and executed the statements one by one. It took less than an hour, as I remember.
You do not need to do it incrementally, you can do it in one step. Only the migration sql will be bigger.
(The other trick was: first I asked DBA's to create a copy of the DB and I did it on that one.)
My upgrade from 4.21 to 4.31 was a disaster. Report seed bundles had to be hand-edited before they would successfully import, undocumented login page redirect changes caused some additional scrambling and BIRT reports are still failing. This was the first upgrade of many to be so problematic.
I'm facing the same problem you had. There are no way to make Seed Bundle action to work well.
About the DataBase migrations, I ran the entire script at once (in my case I have used SquirrelSQL client), and everything worked very well!
Obs.: My database provider is SQLServer (jtds).
I'm waiting HP to provide a solution for this problem... So when it's done, I will upgrade my prod environment.
This is not good. I'm on 4.21 right now and need to get to 4.31 because of the VS 2015 support. As for the report seed bundles, I've had problems with those since around 3.8. FWIW, I encountered a problem with a built-in PCI report and it turned out to be an issue with an incorrect data type. Perhaps you're having the same issue?