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Chargebee will never create duplicate records in Intercom.
When you set up the integration, Chargebee prompts with a list of :
This is to ensure there are no unnecessary records that will be created by Chargebee in Intercom by mistake.
This also applies to cases when you have synced some of your users to Intercom through your custom code, where Chargebee's Customer ID is not associated with a User ID or Company ID in Intercom. For such cases, download the CSV post Data Validation, find the unmatched records which fit the above scenario, and archive those records in Intercom.
For any customer record in Chargebee, which is not available in Intercom, if you have enabled the [create configuration], Chargebee would attempt to create a user/company record in Intercom. While doing so, Chargebee verifies once more to see if there is an existing user/company record in Intercom for the same Customer ID in Chargebee. This double-check ensures no duplicates are created by Chargebee in Intercom.
Related Documentation
https://www.chargebee.com/docs/1.0/intercom.html#integrating-intercom
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