The CSV produced by FC does not know about what contest entries you have entered. In order to edit existing lineups on Draftkings, you need to copy the lineups from the FC produced CSV file, over the lineups you currently have in the Draftkings Edit Lineups CSV file.
This will require you opening both CSVs in Excel / Google Sheets or some other program to edit the lineups. Here is a video of how to do it:
Oh wow that's a lot easier than I thought it would be! Thanks for the video tutorial and help! Good luck in DFS!