Development Activity breaks Sprint indexes

Issue Summary

Performing development related activities such as creating commits, branches, pull requests will cause the related issue to disappear from the active sprint board.

Please note that this behavior cannot be reproduced reliably and the steps to reproduce will need to be repeated several times. 

As of 19.11.20 the bug is reproducible every time.

Steps to Reproduce

1. Start a sprint
2. Create a new issue
3. Add the issue to active sprint by editing sprint field on the issue
4. Transition Issue
5. Create a branch for issue via Jira
6. Create a Pull request
7. Transition Issue

Steps to Reproduce 2

1. Start a sprint
2. Create issue
3. Add issue to active sprint by editing sprint field on issue
4. Transition issue
5. Commit a new message with the issue key
6. Check the sprint board

Actual steps to reproduce

1. Create a sprint
2. Create an issue
3. Commit a new message with the issue key on EVERY devstatus.applink:thread (either make sure with additional logging, or just do it multiple times with some time space between pushes). You have to make sure that the same thread will perform a commit before and after assigning the issue to a sprint.
4. Assign the issue to the sprint
5. Commit yet another message with the same issue key
6. Check the sprint board

Expected Results

The issues should be visible on the active sprint board

Actual Results

Check the Sprint board - the issue disappears from the board

1. In this example, we can see issue AH-3 is added to the Sprint field for AH Sprint 1 but we cannot see the issue on the active sprint board:
   
   
2. Perform a project re-index and issue re-appears
   

It is very hard to reproduce the issue reliably. After countless commits, we manage to reproduce the problem again ( AH-4 this time )

As of 19.11.20 the issue can be reproduced reliably every time, as seen on the following screenshot: 

Checking this SQL output, the database returns correctly which confirms the problem with the indexes :

select cfv.issue as issueid, cfv.stringvalue as SprintNumber, ao."NAME" as SprintName, cf.cfname, p.pkey || '-' || jissue.IssueNum as IssueKey, cf.id As SprintCfid
from
CustomFieldValue cfv,
CustomField cf,
jiraissue jissue,
project p,
"AO_60DB71_SPRINT" ao
where
cf.cfname='Sprint'and
cf.Id = cfv.CustomField and
jissue.id = cfv.issue and
jissue.project = p.Id and
cf.cfname='Sprint' and
ao."NAME" like '%<SPRINT_NAME>%'

Workaround

Use the reindex rest API as a work around for the issues that are impacted: https://docs.atlassian.com/software/jira/docs/api/REST/8.9.0/#api/2/reindex-reindexIssues