Issues not found on reference branch strategy after migrating from 9.2 to 9.3

On 9.2 when project branch was using reference branch strategy as New Code Period, after migration to 9.3 issues stop to show up on new code.

Steps to reproduce:
When on 9.2

1. Set default New Code Period on project to Reference branch
2. Analyse main branch
3. Create and analyse feature branch
4. Commit any change to feature branch which would raise issue
5. Analyse feature branch
6. Commit a change to a main branch
7. Analyse main branch
8. Rebase feature branch on top of main branch
9. Analyse feature branch
10. Search for new issues on feature branch
11. Wrong issues will be shown as per bug in SONAR-14929

Migrate to 9.3

1. Search for new issues on feature branch
2. No issues will be found

QG conditions and issues count is not affected.

Workaround:
Delete feature branch from SQ and analyse it again

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After this bug fix is released in SQ 9.4, if you're still facing this problem in one of your project branches, don't forget to re-analyze the branch and that will fix it.