Steps to reproduce

1. Create a class with two fields: title (text line), related_articles (object relations - browse);
2. Create an object of this class. Give it a title and select 2 existing objects A and B (used articles) into relations field;
3. Via Public API, create an updatestruct where that field is set to link to B, A

...
$contentUpdateStruct->setField( 'related_articles', array(117, 110) );
...

4. Try to update object. It is updated (new version created), but still links to A, B instead of B, A.