This may a browser error where it's reusing the cookie stored for your transaction and being used when you try to pull your second account.
Use the Chrome browser and clear browsing data for all time before signing into TurboTax. Then try to complete the import.
If you are still unable to import it properly, then you do have the option of entering only summaries, instead of transactions.
Here are some directions to do that: Enter Summaries in Lieu of transactions
Additional info on Importing Multiple Accounts.
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