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Well I'd be concerned if the automated system doesn't recognize ur order #. Not saying it's means u won't get ur phone on launch day, but it's just another thing to worry about in the unreliable world of iPhone preorders. All u can do is hope that everything goes smoothly and ur phone shows up on Friday (maybe even Thursday). But I am sure come next Friday there will be people saying they ordered at 3:30am who didn't get their phones, and people who ordered at 3:30pm that did. That's why I hate depending on shipments. I loved the pre-order with in store pickup. It made me feel like I was more in control of getting my device on launch. Anytime there are automated systems, thousands upon thousands of orders all coming in at the same time, and a limited supply, u can't bet that somewhere along the line there are gonna be a few problems. U just have to hope that ur not one of the unlucky ones.
Another thing to check is ur upgrade status for the line u just upgraded. If it shows 5/8/2013 (or somewhere around that date) it's a good sign that ur order does exist.