Is there any reason why you don't use a database?
CREATE TABLE `emails` (`address` VARCHAR(255) NOT NULL, PRIMARY KEY (`address`)) ENGINE=InnoDB
INSERT INTO `emails` VALUES ('user1@example.com')
SELECT * FROM `emails`
DELETE FROM `emails` WHERE `address`='user1@example.com'
These are just infinitely easier and more efficient than a text file...
But if you want to use a text file...
$to_delete = 'user1@example.com';
$file = array_flip(explode(",",file_get_contents("email.txt")));
unset($file[$to_delete]);
file_put_contents("email.txt",implode(",",array_flip($file));
Basically what it does it explodes by the comma, then flips the array so that the emails are keys (and their numeric positions are values, but that doesn't matter), then it removes the email you want to delete and finally reassembles the file. The bonus of this is that it will also strip out any duplicates you may have.
You can use a similar method to add email addresses, just changing the unset line to $file['user1@example.com'] = -1; (to ensure the number doesn't conflict with anything, as that would interfere with the array flipping).
