Hi Spritchet,
My guess is that you could certainly do this with FIRM, but if you are using embedded partitions why not create a new Windows embedded partition installer package and re-run this on the target workstations? This would perhaps be simpler than updating the embedded partition itself. Each server will need a reboot with either approach.
I would personally only go for the FIRM approach for the bootworks partitions which contain files/data which you don't want deleted. Typically this means those those larger hidden partitions which are often used for local image stores.
If you want to pursue the FIRM approach, let us know what automation OS you are using, and we'll dig out the correct file to change for you.