Package feature not finding all Links

I have a master Illustrator file which in turn has individual illustrator files placed in the master. The master is then placed in an InDesign document. When the package feature is used, the placed files to the master Illustrator file are not placed in the links folder, only the files directly linked to the InDesign document are included. Now I know it can work this way, I have a rather large project completed this way. I was wondering if the files have to be in a specific hierarchy to work right? Any thoughts?
Thanks in advance.
Chris

Thanks for the reply.
I could see that of ID, but it is the Preflight feature that has found them in the past. As I say, I just got through with a project that when I did the Preflight Package it placed all 15 of the graphics linked to the master .ai file in the package's links folder along with the master .ai file.
This latest project didn't find them and one thing I see is that the files are in a different hierarchy in the file structure. The last project had all of  the linked .ai files in the same folder as the master .ai file and the latest one does not. I guess I need to do some experimenting.

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