Well, the credits I write, so I decide to use some feature to avoid forgetting. Similarly, I forgot to remove the name of someone whose resource I ended up not using, but it is better than a name left over from what is missing.
The complete sketch - plot, dialogues and etc - I write in the script format to facilitate future modifications. About character profiles, luckily I've never had any problems. I do not even need to write down anything about them. In fact, some of my characters do not even have a predetermined profile, I leave it to the player.
For information on items, equipment, classes and etc. I use the notes boxes of them. As for location information, I use the map note boxes.
I even get confused with skills and enemies, so I do the same thing in their notebooks. "This one will be dealt at level X, when the player will receive the ability Y ..."