If you still have Netflow installed, you many not want to delete the table. But, if you are just trying to remove the netflow data from the DB then you can try these one of these two approaches.
1) Go into NTA settings, under Database settings reduce the number of days to keep the data. Then when the next maintenance is ran, the old data will get removed. Then you can later change these settings back to the days you want to keep NTA data.
2) Or you can use the truncate command to remove the data from the tables. Command "truncate table <tablename>" . This can be ran from the database manager.
Option 1 is your safer choice.