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There is no way to delete and import. Do the transactions show up under new transactions?
On the online version there is no way to reverse or delete a download. If the transactions were showing up in the new transaction column it would be possible to move them excluded column. The excluded column would achieve the same result as deleting the transaction. You mentioned that is 3K transactions. Is it possible to sort the excel file and come up with various expenses etc. The other option would be to create a journal entry to reverse the transactions that were imported in CSV file.