Delete orphaned notes from Elasticsearch index

What does this MR do?

We discovered at !55878 (merged) that there are sometimes orphaned commit notes. Since these are making it difficult to migrate as we can't set the permissions correctly for these and also since you can't actually navigate to a note on a deleted commit there is no point in keeping these in the index.

This change was extracted from a combined MR at !55883 (closed) so it could be merged independently from the migration with some minor changes to broaden it to all types of deleted notes.

Screenshots (strongly suggested)

Does this MR meet the acceptance criteria?

Conformity

• 📋 Does this MR need a changelog?
  • I have included a changelog entry.
  • I have not included a changelog entry because _____.
• Documentation (if required)
• Code review guidelines
• Merge request performance guidelines
• Style guides
• Database guides
• Separation of EE specific content

Availability and Testing

• Review and add/update tests for this feature/bug. Consider all test levels. See the Test Planning Process.
• Tested in all supported browsers
• Informed Infrastructure department of a default or new setting change, if applicable per definition of done

Security

If this MR contains changes to processing or storing of credentials or tokens, authorization and authentication methods and other items described in the security review guidelines:

• Label as security and @ mention @gitlab-com/gl-security/appsec
• The MR includes necessary changes to maintain consistency between UI, API, email, or other methods
• Security reports checked/validated by a reviewer from the AppSec team

Related to #300351 (closed)