Entity Wrapper : how to delete multiple values field?
Well, I solved it. The answer is kind of tricky.

You can't delete a value in a multiple values field. However, you can set it to "empty". When it's empty, it's removed.

Here is the code to use:

// Also, note the -&gt;count() method
for ($i = 0; $i &lt; $user-&gt;field_data-&gt;count(); $i++) {
  $user-&gt;field_data[$i]-&gt;set();
}


This way, values are now empty and the multiple fields have no value left. It's well shown in the UI too and the deltas are correctly handled in the database.