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I'm having issues with all links breaking in a file even after relinking them all and packaging the file. Upon reopen all links are show to be broken again. Additionally, when relinking the first broken link back to the Links Folder, the feature to search for other links in that folder does not work despite the folder containing all links for said document.
This has happened multiple times on different folders. I've even noticed this happening in Illustrator with images linked from the Cloud Library.
Thoughts
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At this point it's unclear if both situations are linked or not.
For your InDesign file - is it just this file - if so
File>Export
Choose IDML
Open the IDML in InDesign
Save the file as a new InDesign file with a new name
See if the issue persists.