Post meta values are strings/text, any internal structure such as arrays or sub-arrays is purely contextual and implied, and generally not a good idea, especially if you want to sort/filter/query for those sub-values.

So you can't make WordPress itself update just the sub-section you want.

Instead, you have to retrieve the entire meta value, change it, then put the entire thing back. There's no such thing as "sub-updates".

You would do it the same way as any other PHP application, this isn't a WordPress problem.

To remove an item from an array in PHP, use unset( thing to remove ).

E.g.

$test = [ 'banana', 'cucumber', 'apple' ];
unset( $test[1] );
// cucumber is no longer in the test array, and the array now has 2 not 3 items