The credit notes in Chargebee can be imported via the Create Credit Note operation.
You can find this under Settings > Import and Export Data > Choose bulk operation. 

The template sheet to be filled is attached below and the reference document for importing it is here. 

Impact: The credit notes to be created would be synced to QBO, to avoid the same, please disable auto-sync and share the Credit Note IDs with me I will prevent them from syncing via backend configuration.