I want to batch convert a lot of files in seperate folders and sub-folders but replacing the original files to save time sorting the files out and the extra space needed for the convert files.
Any software out there that will let me do that?
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I don't think so.
You could make some custom bat/batch file that removes each file after each conversion. But it will be a complex batch.
This is trivial if you have programming skills. This can easily be accomplished using perl or any variety of programming languages.
I've posted several batch files that use ffmpeg to convert videos in all folders and subfolders. You could easily add a command to delete the original file after encoding. But it's dangerous to do so though -- if the conversion failed your original video would be gone. You should at least check the error code that ffmpeg (or whatever program you use) returns to verify that it thinks it converted the video successfully.
I don't even put the converted files ON THE SAME DRIVE and you want to overwrite the original on the fly?