Clean up `noteable_id` for notes on commits

What does this MR do?

Cleans up noteable_id for notes on commits.

This was set incorrectly by a bug in #54924 (closed)

This is a follow-up MR to https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/25278 which fixes the bug

This also adds a batch_size option to update_column_in_batches so that we can update in batches of 300. This is needed to prevent timeouts during update (#58612 (closed))

What are the relevant issue numbers?

Closes #58612 (closed)

Does this MR meet the acceptance criteria?

• Changelog entry added, if necessary
• Documentation created/updated via this MR
• Documentation reviewed by technical writer or follow-up review issue created
• Tests added for this feature/bug
• Tested in all supported browsers
• Conforms to the code review guidelines
• Conforms to the merge request performance guidelines
• Conforms to the style guides
• Conforms to the database guides
• Link to e2e tests MR added if this MR has Requires e2e tests label. See the Test Planning Process.
• Security reports checked/validated by reviewer