I'm dealing with the exact same issue as described by Oyu. None of the above solutions work. I cannot delete a customer with an order or separate the customer from the order (to reassign the order to the appropriate account). Effectively, this customer has an account they created online and another that was automatically generated when they purchased in store. If it has happened once, it is bound to happen again. Please develop a solution to this problem.
Any update to this? Last I heard we're in 2015 and nothing is impossible. :) Hell, we can do real time shipping calculations to Nome Alaska while simultaneously sending out order confirmations in addition to recovering abandoned carts and setting discounts and sale prices all within a second or two; shouldn't be that hard to fix a simple mistake made by humans...right?
Once again, genuine and serious issues with Shopifty directly impacting real customers with busy websites gets utterly ignored - This issue affects us on a weekly basis leaving us with a growing list of dual (or more) accounts for the same customer that can't be reconciled.
It's like Shopify is only interested in signing up small starter accounts - those with busy active sites raising real operational issues impacting their business are just ignored