I'm not clear what you are saying. You simply import the C4D file like any other asset and then can edit it with the respective "Open in Cinema 4D" function. The rest we can't know. Your post is at best vague and generic and lacks any meaningful technical info like exact versions, system info and what have you.
I'll try to be clear for you.
I've recently begun doing tutorials in Cinema 4-D Lite, the version that is embedded in Adobe After Effects CC 2014. I am working on a Mac Book Pro OS X 10.9.4 2.66 Ghz Intel Core 2 Duo. I had recently purchased the book After Effects and Cinema 4D Lite by Chris jackson. While doing the first chapter and tutorial I needed a break after about an hour. Saving what I had done in both programs I quit with the intent to return and continue. Two days later I returned. Opening the AE file first, I found I was not able to access or open the Cinema 4D Lite file in the folder it was saved in. The file was not highlighted and therefore inaccessible. I had to access/open Cinema 4D Lite by going through the Layers menu item and selecting Cinema 4D Lite to create a new layer in the Time Line. This opened the program. Once done, I was able to access the file I was originally working in, through the Cinema 4D Lite program, by selecting Open under File. Once done, I threw out the new Cinema 4D Lite layer created in the After Effects Time Line and continue with my tutorial from there.
However, when I came to a point where I saved the new material I was working on the changes were not reflected in Adobe After Effects.
My question is two folded.
1) Has anyone had this problem re-opening a file in Cinema 4D Lite through After Effects?
2) Has anyone had problems with Cinema 4D Lite not reflecting updated saves in After Effects?
I hope this is no longer vague in its descriptions, generic, or lacking in any meaningful technical information.
The standard workflow works for me. I have no problems.