I just started working with Cineware and Cinema 4D lite a few days ago so I’m not sure if what I am about to suggest will be helpful or accurate – more of a hunch.
It sounds like the project link to the original C4D file may have gotten broken somehow. Try this:
Open your AE file that has the non-updating Cineware layer and create a brand new Cineaware layer – that will prompt you to save a new C4D file. Name it something different than your original C4D file.
With Cinema 4D, open up the original file and copy all your objects into the new file. Save. And see if AE now updates correctly.
Or instead of copying the objects from the old file to the new one, you can try just opening up the old file and saving that as the new one.