After Effects relinking missing Illustrator individual layers

[Abril266504273zx2]

I have opened an After Effects project to do some more work to it, but my Illustrator layers are missing. From my research and previous questions asked here, I supposedly have to click on a missing layer in the project panel > Replace Footage > File > and import the missing file.

But when I do that to a missing layer, it replaces the layer with the whole Illustrator file.

How do I just replace all the missing illustrator layers?  

I originally imported them through importing the whole Ai file and selecting "Composition - Retain Layer Sizes".  Also, I have no idea why the files are missing because I did not make any changes to the name or location of the file / source folder. Any help would be greatly appreciated!!

[Andrew Yoole]

Has the Illustrator file been changed in any way?  It sounds like the Illustrator layers may have been grouped into a single layer, or the colour mode of the Illustrator file has been changed from RGB to another colour space.

Quick way to check - re-import your Illustrator file to AE as a composition and see if the layers are all seperate.  If they are, it's not the issues above.  If it will only import the file as a flat Illustrator image, its most likely one of the issues above.