This article is from the Final-Fantasy and other Square Soft Games FAQ, by email@example.com (Nick Zitzmann) with numerous contributions by others.
After finishing Vagrant Story, the game prompts for the game to be saved
again. This save data works just like EX save game data in Parasite Eve;
it begins the game again with the same character you built up when you
finished the game.
The clear data also retains all of the items you acquired the previous
time around, except for miscellaneous items. That's right; if you forgot
to use some of the grimoires or elixirs, there's no way to retain them.
The advantage of the clear data is the Rood Inverse. All of the doors
which were sealed with the Rood Inverse the first time through the game
are now unsealed, which allows you to reach the 20% or so of Lea Monde
which you can't reach the first time through the game. Behind the Rood
Inverse-sealed doors are the Gold and Platinum Keys, which with the
Silver and Steel Keys, allow full access to the Iron Maiden bonus