Programmatically update field collection data in custom entity
Please use below code for update existing field collection data 

//$item_id load item id from your node
//enter_update_field_mechine_name replace with your field name  
  $field_collection_value = field_collection_item_load($item_id);
  $field_collection_value-&gt;enter_update_field_mechine_name['und'][0]['value'] = 'update text here';
  $field_collection_value-&gt;save();


This code worked for me
Thank you