after importing the aep project and use some elements in your comps.
Go to File -> dependencies -> Remove all unused footage
Go to File -> dependencies -> Reduce projects
* make sure to backup your file before.
lets know if that helps
I don't know about a solution and wish someone could suggest somethings. sounds like there could be a script for this...
in the meantime I can suggest 2 workarounds I use:
1. import the project, drag what I want to where I want and then select the compositions I want keep and select Reduce Project, Consolidate and re-order things in my project window through a script or manually.
2. open another instance of Ae and select just the composition I want to keep and reduce project, then save. then I import this to my main instance of after effects where I need those assets imported to.
Selecting the composition and reducing the project works.