The merged order leaves your open orders by itself, and any order can be archived from its window

When Tacey merges two orders, the order that was merged away now closes in Shopify on its own, so only the order that keeps the items stays in your open list. If you still owe the customer a shipping refund, the order stays open, carries a tag saying a refund is owed, and closes as soon as you have confirmed the refund. This is on by default, and you can turn it off with Archive the merged order in Merge settings. A second switch there, Archive cancelled orders once refunded, closes a cancelled order only once its money is settled. That one is off by default.

Archive and Unarchive buttons also appear on an order's window in Tacey. Tacey refuses to archive an order that is unfulfilled or still owes money, says why, and adds one Order changes entry for every order it closes. Nothing is ever deleted.