During flight testing the manufacturer tests the aircraft with every access door, fairing, etc, etc that they figure will be knocked off by accident or fall off due undetected wear and tear or as a result of not being closed or secured properly and puts all the data in the Configuration Deviation List (CDL) which is an appendix to the Flight Manual.
It is very expensive and time consuming to go back and redo a test for some bit that gets knocked off that nobody thought of first time round. It can be done whilst testing a variant of the same model and possibly the data can be read back to previous versions.
The Japanese -400SR's were certified without winglets and are a unique variant of the 747-400.
As someone wrote above Boeing no doubt figured you would only damage one winglet at a time