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Per your description, I understand that some issues are not appearing to be selected in the Linked issues drop-down.
I would check the following details:
1 - Check if your user has the Browse Projects, Edit issues, and Link issues permissions in the project of the issues that are not appearing, using the permission helper.
2 - Check if you are able to access the issues that are not appearing in the drop-down, just to make sure it is not configured with a security level.
If that information didn't help, please provide us an issue that you are not being able to link with the screenshot of your permission helper results.
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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