>>98966609I like to think that after escaping from the Cell, her Archive moved to within the castle she found and decided to make her lair. The one all of Advent is inside of in their promo art and the one seen in Shiori's 3D.
It exists in a pocket dimension similar to Amelia's office or even the Cell. Humans aren't likely to just wander in. As such, it's a safe space for herself, her friends and her inky companions. If Shiori wants, she can use her texts to try to create a specific design for an ink being. Evolution also takes its course and new variations pop up.
Should she need, she can use them to observe or in direct combat. Even learning how to bring some out of that dimension and into the full world.