How to delete only user meta value (not key) from usermeta table in wordpress?

Just remove the ID then.

$images = get_the_author_meta( 'images', $user->ID );
$images = explode(',',$images);

$images is an Array isn’t it? Then I hope this one can help you.
https://stackoverflow.com/questions/2448964/php-how-to-remove-specific-element-from-an-array

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