Solution : https://service.sap.com/sap/support/notes/365327 (SAP Service marketplace login required)
Key words : 
additional key words va02, additional bom components, newly created item, free item numbers, settings sales order, sales order items, sales order, unwanted items, sales document, added manually
Related Notes : 
       
| 418336 | Manually maintained components with configuration with set | 
| 380845 | SET with manual changes: Double items | 
| 361549 | Configuration lost during changes III | 
| 358119 | SET with manual changes: confounded items | 
| 334782 | Configuration - double sub-items II | 
| 332577 | Configuration is lost for changes II | 
| 329927 | Configuration - duplicated sub-items | 
| 325706 | Configuration is lost when you make changes |