Spent three hours via screen share with adobe and after seeing the problem they tried to blame my workflow.
Its a flaw in the "Save Artboards to Separate Files" option when saving in AI.
Even though each file created from this option will contain only the correct layers for each Artboard (opened in AI). They for some reason contain a "settings" (as not really explained by adobe) that contain all the original layers (containing no data) when imported into AE.
The "correct" workflow Adobe told me was as follows;
1) Use the "Save Artboards to Separate Files"
2) Go through and re-open these Individual files
3) Re-save and re-name all of the new files.
Some how this clears these mysterious "Settings" but when your dealing with over 100 artboards its the dumbest **** Ive ever heard.
They however were unable to explain how re-saving it changed the file or why a re-save was any different "Save Artboards to Separate Files"
Thanks @Adobe for sending me an adobe basic video when I showed you this.
Cant wait for the day I can switch to any other applications.