How to automatically convert MKV to MP4 and retain the Subtitles and Chapters

This is awesome but i have one question. Can i do this to my current profile, but it NOT run on anything it has already ran on? Case is, i have already run MCE on anything that was over 6mbps bitrate. If i do this, will it do those again or see that it has already encoded them once and not do it again. Hopefully the latter. Thank you!!!