Shopify does not currently have a function to merge multiple customer accounts into one I am afraid.
The only suggestion I have at the moment would be to apply a tag to customers who do have multiple accounts so you can at least gain some clarity when viewing their profiles.
Although I cannot provide any guarantees at this time, I will submit a request for this feature. :)
This is so dumb!
We have an increasing number of customers (growing on a weekly basis) with at least 2 accounts generated when they mis-key their own email address.
If you try and edit the wrong email address back to what it should be you get a error message "Email has already been taken". So you and the customer are simply left hanging.
Those customers will not receive any transaction emails (as its going to a non existant address) and whats criminally worse is you cant fix it !!
Shopify seems OK for toy users but when you grow into a real eCommerce site the holes appear and you realise it simply is not up to the job...
Oh and this issue it s least three years old - THREE YEARS!!!!!
There's a thread on this here: https://ecommerce.shopify.com/c/shopify-discussion/t/merge-two-customer-accounts-into-one-276831
The best way to fix this is to submit (and continue submitting) feature requests, which you can do by emailing Shopify via their form: https://support.shopify.com/customer/portal/emails/new
Or here: email@example.com.