I filed jointly with my wife but her ITN had expired and the IRS recalculated my tax return to a lower amount. I have her new ITN, how do I get the full refund?

File an amended tax return with her current ITIN.

See this TurboTax support FAQ for amending a tax return originally completed and filed using TurboTax - https://ttlc.intuit.com/community/amending/help/how-to-amend-change-or-correct-a-return-you-already-filed/01/25588

BEFORE you start the amendment process you have to change the return to match what the IRS changed and only then should you start the amendment process. 

Look at the form 1040X …

Column A should have the figures  AS ADJUSTED BY THE IRS, Column C the corrected figures and Column B the differences between the other 2 which needs an explanation on page 2 of the form 1040X.

If you completed it correctly you will see an entry on either line 16 OR 18:

On line 16 should be the amount you paid with your original return. 

On line 18 should be the amount of your original refund you received.

Then you will see your extra refund on line 22 OR  the new balance due you need to pay on line 20.