Originally Posted by
SEA1K4EVR
Yes you get them back. If you make the change over the phone you can just tell the agent you want to upgrade the new flights and they'll re-apply the instrument for you. I don't know how much pain that would cause... doesn't sound like much

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Although in practice they'll likely take a different instrument and you'll have to request a redeposit of the original.
octeckels and I have had to request several award redeposits recently. None have shown up automatically, but all have appeared back in the account within a day of submitting an award redeposit request on the website.