I want to increment 1000 by 1 for all records making all the rows unique.
This cannot be done -- flat files do not have rows. Ever. They have records, and you started off saying so -- but then you switched to rows. Furthermore, your title indicates you want to increment one column of the flat file. This means you are changing one -- and only one -- byte, since (unlike data bases) a column in a flat file is a single byte.
So are you wanting your records to be
or something else? You certainly cannot make 9000 records unique by just changing one column of the flat file!
And what have you tired yourself so far? What SORT product are you running at your site? What tools do you have available to help you with this task?