I am wondering if there is a way to merge more than 2 customers at a time through Shopify? If not I, and I assume many others, would appreciate a change being made to allow this. Please like this to move it up to the top so that Shopify developers might see this, and implement a change.
Unfortunately you have to manually do it over and over. You should chat with Support and ask for an official feature request. Staff aren’t in the forum anymore.