The problem the integrations have is that while you consider it a "duplicate" the system has different records across each system.

"merging them" destroys the relational integrity.

Other firms do the following :-

Through merging Retail Express does now allow complete deletion of a customer with order history. This will create issues for data integrity and must be done :-

1) In batches and only when systems and processes are not busy, definitely not during sales or promotions
2) Performed on mass as you are about to create a lot of additional work
3) After running IMMEDIATELY notify downstream systems such as Shopify, Mail, ThankQ, and customer facing systems and re-sync the profiles to hopefully re-link successfully. This may take several days to complete during this time it is critical no further merge and data destruction takes place

Prior to merging 
 
we have an alternative procedure to be followed to “archive” duplicated clients and not destroy data integrity
We can do this by setting the last and first names to an underscore first, then you can use these to merge OR set the email address with an underscore and .CustomerID suffix at the end to ensure it does not get used.
By these simple changes you can dramatically reduce duplicates in your system and save on downstream costs like ThankQ .

Shopify uses the customer email as the primary key but this means there is only ONE record in Shopify for the many in Retail Express. The system has connected only ONE record. When you delete data you are sometimes deleting the "wrong" one and this results in orphaned orders unable to send.

The Mystery of the Duplicates
This is about finding who is the real one and thinning out all the duplicate characters. When we run our routines we use a deeper analysis including order data and both addresses to locate the best one to “remove” but do not delete any data. The Merge process was added to Retail Express without consideration to external or internal systems. You have removed / altered audit logs and business records when you use it.