I realized that there also was a Sony Corporation folder in the Preferences folder that Sony's own uninstall script doesn't remove. This folder contains EBL's database
Once that was removed the program could start again, even though it is without any books in it.
But if any of you get into the same trouble, beware!
EBL only syncs one way.
I connected my reader expecting it to sync my books and notes on the reader back to EBL. But nooooooo
Everything on the reader was deleted.
EBL really is a big pile of *beeep*