For output I have only PDF. For input I have a range of options - AI/DXF/AI/EMF/PLT. 

Inkscape has DXF both via built in and also the BetterDXF plugin. It can also do SVG of course which can then be converted again to AI potentially with pstoedit. 

Inkscape has commandline options for batch processing but not for DXF AFAIK. It tok me a while to figure that out. DXF export is support but via GUI. 

Anyway, the simplest thing is to use pstoedit rather than Inkscape for this task. 

I'm just putting this out there on the hope that this gets picked up by Google when people are searching for converting vector files for free because at the moment Inkscape is coming up as a suggestion in many search results and I ended up taking a lot of time trying to figure out how to write a batch file when at the end of the day I should have been using pstoedit. 

AI worked better since DXF will need to you tell it the scale (i.e. mm or cm). Successful command for me was: 

 .\pstoedit input.pdf -f plot-ai out.ai

Hope this helps someone out there