One thing that stumped me for quite some time is the reliance on FixVersion/Release. If your parent issue has a FixVersion/Release that was NOT selected when configuring the portfolio/plan, but the child issue has a FixVersion/Release that WAS selected, then for some reason Portfolio/Plan doesn't include the parent issue cause it doesn't meet the FixVersion/Release settings. So I suggest you check your FixVersion/Release settings for any issues not showing up and cross reference it with the selected Releases in your Portfolio/Plan.
I would love if the tool was smart enough to bring along any parent issues regardless of FixVersion/Release, but not that way currently.
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