if you already import the AI file to AE you can't add new layers in illustrator, it will not show up in AE, the solution is to reimport your AI file again. and if you want to replace the layer you must be sure it has the same name, and it's best if you edit the existing layer only so don't delete or add layers
When you have imported an Illustrator or Photoshop file as a comp and you need to modify a layer using the Edit Original (Ctrl/Cmnd + e) on the layer in the timeline will always work.
If you need more layers and you want to keep them lined up with the artboard and you want to retain layer size then you either have to start over or save the modified Illustrator file under a new name, Import the file as a comp retaining layer size, then open the comp AE creates, copy the new layers and paste them in the timeline created by the original file. This will maintain their position and not foul up any animation you have already added to the project. I do that all the time. I'll end up with five or six AI files imported as a comp that only contain the new layers, and the original comp created by the original with the new layers added by copy and paste. That is the only reasonable way I know of to add a bunch of layers to an existing comp created from a layered file. The other way just takes way too much time.