It's actually really easy to update to a newer fresh version of PSDK! All you need to do is go to your Data\PSDK folder and move over the files you wanted. So, if I wanted to add all my Fakémon again, I would copy, paste and replace the PokemonData RPGXP file from the outdated buggy version into the new clean one! And just like that, the Pokémon data is all there. (Don't forget your graphics, and cries!)
"But the names, descriptions, and species are still official Pokémon!" you may be saying. Well, to fix that you need to go to your outdated buggy Data\Text folder and copy and paste that into the new PSDK's Data\Text folder as well. (Specifically the files named 100000, 100001, and 100002 in this case!)