Not sure if the problem still occurs, but we were facing the same issue and solved it for us. have a look at this solution: https://community.atlassian.com/t5/Answers-Developer-Questions/Issue-links-missing-from-REST-search-and-issue/qaq-p/530279
For others with the same problem: the problem depends on the visibility of the linked issues field in the field configuration of your project. It might be not visible!
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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