Usecase #1
If you use Convert to Issue on a sub-task, the issue is removed from the current sprint and completely disappears from all reports (e.g. sprint report, burndown report)
Usecase #2
If you change an issue's metadata so that it no longer matches the rapidboard's filter query, it completely disappears from all reports (e.g. sprint report, burndown report)
(I have filed a GH Bug: https://jira.atlassian.com/browse/GHS-8457)