For a Project with BlazeDS I had to work with updating and reloading Tree component data without breaking the User Experience (all nodes closed when data reloaded).
Instead of keeping tabs on “which node was opened before?” and “what was the scroll-position?” I found a way to inject the new state of the Tree component data into the existing data provider.

See article here if you are interested.
BlazeDS and Smooth Data Injection – Reloading the Tree View Data Provider without breaking the User Experience – http://bit.ly/92h7on

Hope this is of help as well.

My trick to using array collections is a custom made PHP class that while transmitted through AMFPHP behaves as a native array collection, instead of an array.

When I create the array tree in PHP, before passing it to Flex, I convert each array node to ArrayCollection using this class:

class ArrayCollection {
	var $_explicitType = "flex.messaging.io.ArrayCollection";
	var $source = array();

	function ArrayCollection( $array )
	{
		if( !isset( $array ) )
		{
			$array = array();
		}
		$this->source = $array;
	}
}

Usage would thus be:
$node = new ArrayCollection( $myarray );

Hope this helps.