To help identify the problem, add a row number field to each row in the QlikView table. That will give you at least one field that is unique on each of the duplicate rows. You can do this without reloading the entire document. Here's an example-- First, save a backup copy of the report that you are working on. Assume that the table to which you want to add a row number is named REDFLIGHTS. Add these rows to the top of your loadscript:
Add Load RowNo() as REDFLIGHTS_RowNo, * Resident REDFLIGHTS;
Drop Table REDFLIGHTS;
Rename Table REDFLIGHTS_X to REDFLIGHTS;
Then, from the menu, select File->Partial Reload This will run the five lines you added to your loadscript and it will build a new table inside the document that is identical to your original table but with a rownumber field, REDFLIGHTS_RowNo, added to the table. Now, in a tablebox that includes the rownumber field or in a chart using the key fields as dimensions and using a count(REDFLIGHTS_RowNo) expression you will be able to identify the duplicate rows in the table. At that point you will have to figure out how to eliminate or handle the duplicate rows when data is loaded. Remember to remove the five lines from the top of your loadscript before you next try to reload data.