There seems to have been a loss of information about the build options for the S6. It used to have its own page but has now been combined with others under the 3D Printer and Engraver boards section and the build options has been moved to a page (Uploading firmware) collecting tools settings for all the boards. The original page had a screen shot of all the settings but now the text description omits the optimization and runtime library settings. Not to say the defaults won't work, they just are not the best.

I don't think the board is damaged. The S6 doesn't have a USB-to-serial chip like some others because the chip is fast enough that the kernel can run it directly. So the same hardware that gives you the COM port should be in good shape to run the DFU mode.