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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.
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