This can be more complicated than you might think.
When you package a file you are making a copy, and at the same time you are making copies of the links in a new links folder and changing the link path to that folder in the new file. If you edit the original file youare working with the original links, not the copies, and if you are working with the packaged file you are using the new links in the links folder. Did you add another link to the file? If so, did you make a copy and add it to the links folder?
What I usually do is .... once I think I may be through with a file, I package it and then to keep from getting everything confused, I delete the original file and work from the packaged file. Then when I need to make a change or add another link, I save my work but do I need to package it again to link the new graphics? To answer your question, I did not make a copy and add to the links folder. ???? I am finding that weeks later when I need to visit this file again, I am having search computer to re-link graphics that I thought was already linked.
If you are working on the new package then you can just copy the graphics into the new Links folder and use File>Place and select the file from the links folder.
All packaging does is gather up all the links, fonts and indesign file that are in use - saves them and links them to the new links folder.