You fell for the old ''optimized repository'' issue.
Actually is is not an issue, but a new ''feature'' of ALM/QC11 and later.
HP has updated the repository to a newer ''optimized repository'', where it works a little more like a configuration management system -- it tries to identify duplicates and only stores once then uses reverences to duplicates - it should use less disk space and be faster.
As soon as you finish upgrading a project, then activate it, the ''Repository Migration'' process starts automatically int he background. It may take a few minutes to a few days for each project, depending on how large it's repository is. You can monitor the progress from Site Admin with eh new Tools/Repository Migration tool.
During migration (less than 100%), you cannot Copy or Export your project, and users may notice attachment/repository ''issues'' when they happen to work with a record whose repository items are currently being migrated.
When complete, the project repository folder for a given project should only have the ''ProjRep'' folder and the dbid.xml file. If a project 's repository migration is started, but not finished yet, you would see the new ProjRep folder, and would notice some old folders are missing, but not all of them.
So, it does sound like the upgrade you did is progressing and you should not need to do it over. check the Repository Migration status.
If a migrations seems to get stuck at 97%, say, you need to look at the notes referenced in the repository migration status tool window, go to the log file referenced, and see what it says -- usually it is a file or two that it can't/won't delete, so you need to do it.