I've updated the imported Illustrator file that I am using in After Effects with some new layers and other stuff, but the changes are not seen in my compositions. How can I get my compositions to recognize the changes?
Right click the Illustrator file in the Project panel and select Reload Footage.
If you imported your Illustrator file as Footage, then that will work with no problem; you'll see your new layers and all changes etc.
Unfortunately if you imported your Illustrator file as a Composition (meaning you have a separate project resource for each layer as in the above screenshot) reloading those layers won't import your new layers. Also if you imported with Retain Layer Sizes, your layers within the composition won't update they're position, only the content.
The only real solution to that is to reimport as a new composition and copy over the new layers to the original composition.
I had similar problems updating an Illustrator file and it wasn't updating. After trying the methods above, I then deleted the source file in the Project window. The warning box told me that the element was being used in (x) compositions. I deleted anyway, then immediately performed 'Undo'. Like magic, the file finally updated correctly. Note that this was a layer in an Illustrator file that I had previously imported as a composition along with the other layers in the same file.