I have an issue where I had an existing library. Then I created a new library and suddenly half of my components in my original library were linked to the new library I created. Even though the new library did not contain any of the first librarys components. I then unpublished the new library. Now I have components that say 'Library is missing'.
I have about 50 projects that rely on using this library. If I update any components, I will have to go through all projects and fix them individually. That is unacceptable. Please help. 
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How did you create your new library? It sounds like you used Save As... which preserves all of the internal component IDs, so it's a clone of your original library.
The first thing you should do is Re-Publish the library to restore the links.
To create a separate, new library, copy all of the components on canvas and paste them into a new doc. Select the Linked Components in the Assets Panel, right-click > Make Local. Then Publish to a new Library.
Hope this helps,
Randy
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