​@Gayani_S can you help me in this case? 

Hey ​@Serkan_Zararsiz, thank you for reaching out and apologies for the delayed response! 

I reached out to our support team about the issues you’re experiencing, and here’s the response they provided:

The issue you're experiencing could be due to how Figma handles component IDs when files are moved or copied. When you import files into a new workspace and publish them as libraries, Figma assigns new unique IDs to components, which can break the original links.
Here are some steps and considerations that might help:
 
1. Check Component IDs: When components are moved between files, Figma assigns new unique IDs. This means that even if the components look the same, they are technically different in Figma's system. Unfortunately, there's no direct way to relink them automatically if the IDs have changed.

2. Review the Import Process: Ensure that when you imported the files, you maintained the original structure as much as possible. If components were copied instead of moved, this could lead to ID changes.

3. Manual Relinking: While manual relinking is not ideal for a large project, it might be necessary if the component IDs have changed. You can use the "Select All with Same Instance" feature to speed up the process by selecting all instances of a component and swapping them with the correct library component.

4. File Upload Sequence: The sequence in which files are uploaded and published can affect the linking. Ensure that the library files are published before the working file is linked to them.

5. Naming and Structure: Consistent naming and file structure can help, but they won't affect the underlying ID issue. However, they can make manual relinking easier.
 
Unfortunately, if the component IDs have changed, there isn't a straightforward way to automatically relink them. You might need to manually update the instances in the working file to point to the correct components in the library.

The really important foundational thing to consider about libraries, especially moving them, is that connections between main components and instances are based on the file in which the main component lives. If the library file they were given was the exact same original file the previous team pulled all the instances from, the connections should remain. This holds true no matter where you move the library and working files. However, if the library is a copy or exported/imported as a .fig, the working files will still point to the original library file and the library swap feature will need to be used on each working file to point the instances in those working files to the new published library.

Please let me know if this helps or if you have any further questions, happy to help out further! 

Thanks for the reply!
I ended up fixing it using the missing library and library swap feature. Over 90,000+ components were swapped in the process, so I’m crossing my fingers that everything worked as expected.
 

Hey ​@Serkan_Zararsiz, that’s great news! Swapping over 90,000 components is no small thing. If anything does seem off or you get stuck again, you’re welcome to reach out to our team with your file link using this form. They’ll be happy to dig in and see what’s going on.