I had been doing some testing with Prestashop on a subdirectory in a website (mydomain.com/prestashop/). I tried to import categories via CSV several times and kept failing for many reasons. The result of this is that the database is pretty full of deleted categories.
I decided to give Prestashop Store Manager a try. I set it up and all the deleted categories are showing up as root categories.
So, I'm thinking I would probably be better off learning Prestashop Store Manager with a fresh installation of Prestashop. I set up another installation of prestashop with another database at http://www.mydomain.com/prestashop2/