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I was sent the answer: https://answers.atlassian.com/questions/39140034
The limit on the amount of issues you can load into your plan is 5000. However there is a hierarchy limit of 2000 which is the limit on the number of items that we are willing to render.
So if your epics (+ initiatives if you use them) are < 2000 then we’re able to show you the epics level. If your Initiatives + epics + stories are > 2000 then we are not able to show you the story level (either by expanding epics or with the hierarchy level drop-down)
You can check the number of issues Portfolio is trying to bring over from the "confirm what's in scope" page of the wizard. To the right of "Deselect all" there is a count of how many issues have been selected. Note that this only represents the total number of issues if you are viewing this scope from the highest level of hierarchy as it's a count of the current filter.