You can drop the MySQL column manually, then re-add it with the same properties. The rows will be reordered.
Alternatively, use these commands:
SET @count = 0;
UPDATE `users` SET `users`.`id` = @count:= @count + 1;
Replace users
and id
appropriately.
You can reset your auto incrementing id column also with:
ALTER TABLE `users` AUTO_INCREMENT = 1;
Where users is replaced with the name of your table.