There's code in SDL_RecreateWindow specifically to handle SDL_WINDOW_FOREIGN, but it appears to have been overlooked in the allowed_flags constant.  This causes the line

    window->flags = (flags & allowed_flags);

to strip SDL_WINDOW_FOREIGN from the window's flags, which breaks some code in WIN_WindowProc in SDL_win32Events.c that treats foreign windows differently.  This can be trivially fixed by defining allowed_flags as 

    const Uint32 allowed_flags = (SDL_WINDOW_FULLSCREEN |
                                  SDL_WINDOW_OPENGL |
                                  SDL_WINDOW_BORDERLESS |
                                  SDL_WINDOW_RESIZABLE |
                                  SDL_WINDOW_INPUT_GRABBED |
                                  SDL_WINDOW_FOREIGN);