Overwrite existing files, Have app overwrite every video on a drive or folder which user defines and have application convert every file to one standard file-extension/-type making a hierarchy of many different file types a thing of the past.

This function in collaboration or working with the already built in feature use only when CPU is idle, would make it perfect in my case, having the pc on at all times but not always using it. Having ripped so many videos and troubles viewing them all when they differ and certain players does not play the filetype even if it appears the same, as a different file of the same type.
What I mean is, a .mkv file can have different codecs, I want all videos converted to the same .mkv (version if you will) so if the WDTV player can play one .mkv file, it should play the rest of the .mkv files not just some .mkv and other .mkvs not.