It looks like I'm not the only one seeking to merge duplicate customers. It seems this has been requested for years now with Shopify claiming it's too complicated. I used Square for years before moving to Shopify and while there aren't too many things I miss about Square the ability to merge customers is one of them. If it's not too complicated for Square to do it then how is it too complicated for Shopify which is certainly a more powerful platform/POS than Square?
I found this method to merge customer data on Shopify, hope it's useful for you.
By the way, If you have any trouble while doing business on Shopify, this website: Avada Commerce would be useful for you.
Hope it helps!