Stačí mít účet se svými klíči.
Uložit každý $key
v poli ve vašem while a nakonec spusťte dotaz, který říká
DELETE FROM tabel WHERE key NOT IN (listofcommaseparatedkeysgoeshere)
$arrayThatYouNeedToTest = array();
$handle = fopen($file,"r");
fgetcsv($handle, 1000, ",");//skip first row since they are headers
while(($fileop = fgetcsv($handle, 1000, ",")) !== false) //read line by line into $fileop
{
//read array values into vars
$item1 = $fileop[0];
$item2 = $fileop[1];
$key = $fileop[2];
// and a couple more
// now INSERT / UPDATE data in MySQL table
$sql = mysql_query("INSERT INTO table (item1,item2,key)
VALUES ('$item1','$item2','$key')
ON DUPLICATE KEY UPDATE item1='$item1',item2='$item2'");
$arrayThatYouNeedToTest[] = $key;
}
$stringThatYouNeedToInspect = implode(",",$arrayThatYouNeedToTest);
$queryYouREALLYneedToCheckFirst = "DELETE FROM tabel WHERE key NOT IN (".$stringThatYouNeedToInspect.")";
//$result = mysql_query($queryYouREALLYneedToCheckFirst);