I have tried the following steps with 4 layers, and it seemed to work.
- Name the file with the state 1 set,
your-filename-1.ai
and the file with the state 2 set your-filename-2.ai
. Make sure they are in the same folder
- Open After Effects, click
File -> Import -> File...
and click your-filename-1.ai
. Make sure the checkmark is checked as shown below:
To keep all the individual layers, set Import As:
to Composition
.
3. Now you will have a composition in your project panel named your-filename
and a folder named your-filename Layers
that contains all the layers.
5. Now you can open the composition and check Frame Blending -> Frame Mix
for every layer that you want to tween.
6. Don't forget to enable frame blending. The image below shows how to do this:

Now you have an animation from state 1 to state 2. To change the animation playback speed you can use time-stretching on a layer-per-layer basis.