Hello there, pjmitchell55.
You're right that reconciliation reports won't export when converting from QuickBooks Online (QBO) to QuickBooks Desktop (QBDT). However, all reconciled transactions from your register will be marked as reconciled on your QBDT account.
See the limitations when you convert from QuickBooks Online to QuickBooks Desktop article to know more about the changes upon converting.
On the other hand, if you'll have incorrect beginning balance and unreconciled transactions, you can fix this by reconciling multiple months at the same time.
You can always get back by commenting below if you have any follow up questions about this process. I'm here to help. Have a great day.
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