If  you reimport QuickBooks data a second time, you must first delete the information that was incorrectly imported.  I recommend that you first backup the data and then "Omit" the checks (Options>File Management Utilities>Omit/Keep Checks>enter the starting and ending dates)and then "Delete" the checks (Options>File Management Utilities>1. Delete ALL Omitted Checks).  Once this has been completed import the data again.