I've traced deeply into Xyster and apparently the child entites get deleted because they are missing from the $_items array and are therefore always deleted when the parent entity is saved.

I've written some code to unlink an entity from a set. This does almost the same as a remove, but doesn't delete the unlinked entities when their parent entity is saved. Here follows the code. I left a commented line in in Xyster_Orm_Set::unlink(). I _think_ that unlinking an entity does not make it 'dirty', so I didn't mark it as such. Since the parent relationship also needs to be broken in all the children that you unlink(), the entity gets marked as dirty anyway...

• Xyster/Collection/Abstract.php line 39:

     /*
      * The collection of unlinked items
      */
     protected $_unlinks = array();

• Xyster/Collection/Abstract.php line 181:

     /**
      * Unlinks the specified value from the collection
      *
      * @param mixed $item The value to unlink
      * @return boolean If the value was in the collection
      */
     public function unlink( $item )
     {
          $before = $this->count();
          foreach( $this->_items as $key=>$value ) {
               if ( $value === $item ) {
                    unset($this->_items[$key]);
                    $this->_unlinks[$key] = $value;
               }
          }
          return $this->count() != $before;
     }

• Xyster/Orm/Set.php line 159:

        return array_values(array_diff(array_diff($this->_base,$this->_unlinks),$this->_items));

• Xyster/Orm/Set.php line 251:

    /**
     * Unlinks the specified value from the collection
     *
     * @param mixed $item The value to unlink
     * @return boolean If the value was in the collection
     */
    public function unlink( $item )
    {
        $unlink = parent::unlink($item);
        if ( $unlink && $this->_entity ) {
           // $this->_entity->setDirty();
        }
        return $unlink;
    }