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1) Already linked incidents do not show visually in SPIRA Team as linked when clicking on "View Incidents" link. They do correctly show the linkage in the Incident Summary Report.
2) Under Requirements Coverage, the status tool tip does not reflect the correct number of test cases linked or the Pass/Fail status.
3) When we delete a test case it still shows up in the Requiremnets Traceability Report
1) In a Test Run, you will only see incidents that are linked to the Test Run itself, not those that may be linked directly to the test steps. That is normal.
2) Could you please log a support ticket with us, providing the version number of SpiraTeam as well as a screenshot. There were some issues in early versions of v3.1. If you're not on v3.2, we'd recommend upgrading.
3) Same as answer (2), please make sure you're on v3.2, latest patch.