In JIRA Portfolio, it allows you to put the story points for epic as well. However, for scheduling it only picks up the story points of stories within that epic.
Is that the right understanding?
If so, what role does the epic estimate play in deciding the timelines?
The estimate on the Epic's story points do matter, and help with scheduling. However if you're at Story Level only, you won't see a difference.
Can you confirm what situation you're seeing exactly and what version of Portfolio you're using?
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