The problem in DocBlock file that it creates a temp .txt in temp folder, so what you need to do is delete this files before editing programmatically. There is a command in DeleteFcn in callbacks of the DocBlock itself called "docblock('close_document', gcb);". All you need to do is add this line to your code before calling set_param command like so:
DocBlock = find_system('Model', 'SearchDepth', 1, 'Name', 'DocBlock');
DocBlockHandle = getSimulinkBlockHandle(DocBlock);
B = get_param(DocBlockHandle, 'UserData');
B.content = 'Test DocBlock update';
docblock('close_document', DocBlockHandle);
set_param(DocBlockHandle, 'UserData', B, 'UserDataPersistent','On');
save_system('Model');
