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Remove old indexes from ci_pipeline_variables

What does this MR do and why?

Following up on !137777 (merged), we want to remove the old indexes that aren't using the partition_id.

Please note that the unpartitioned Primary Key Index will be removed when we swap the primary_key to the composite one

MR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

Related to #429000 (closed)

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