can you explain the step by step of what you want to do?
from what I understand, you want to encrypt some folder say like Graphics\Titles and make your game use it, while the other folders like Graphics\System is still unencrypted?
if that's so, I don't think you could do that... since the engine encrypts the Graphics folder as a whole...
Just take out those folders before you encrypt the project, and after you're done extract it and create your own Graphics folder.
You mean like encrypt everything then put the non-encrypted folders back? I tried that before, it didn't work... at least not without modifying the scripts since by default, the load function will look for files inside the Encrypted Archive if it exists... so when you already have the Game.rgss3a file, the game will look by default inside of it for Graphics and Data...at least that's what my tests seem to come up with...