You don't. It works as it is supposed to. Once such a file has been imported, AE only retains a link to the actual AI layer. It doesn't care what else happens in the file after that. You have to manually import your new layers and insert them where you need them.
How can I manually import new layers?
The normal File --> Import will do just fine, I suppose?
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This is one of the gotcha's of working with layered files. If you add something later, you'll have to import it separately (when importing, choose "Footage". Then select "Choose Layer" and select the layer you'd like to import.
Depending on how much animation you've done with the rest of your imported artwork, it may take a little work to get this new layer into the correct placement. Occasionally I'll find it's easier to re-import the whole thing as a composition, just to get me all the appropriate placement. I'll then typically grab the new layer, along with a copy of one of the layers I'm already using in the project, and copy/paste those into the comp I was already working in. With a little parenting, copy/pasting of Transform properties, etc., it's pretty easy to make sure your new layer gets to exactly the spot it's supposed to be, relative to all the other layers you already had in place.
All of this is to say... try to avoid adding layers after the fact whenever possible. It's a bit messy, and can get pretty confusing if you're dealing with complex artwork. As much as possible, try to plan out your intended animation when you're still in Illustrator, at least enough that you can anticipate the various distinct pieces you'll need, and how you'll want them broken up once you get into After Effects.