As they are two seperate nands, no, what you do on one nand is independent from the other. To do something like that you'd have to find a way to force the switch to mount two nands at the same time, which I don't think is possible at all.

I guess you could backup the sysnand from rcm, then create a second emunand partition from that sysnand backup, then use cfw on the new emunand to backup the games.
There's also a windows tool that can extract games/updates as nsp files when you mount your nand/backup to the pc (I never could get it to work myself, but plenty others have managed).

Can't remember what it's called, but just look in the tools or tutorials section and you should find it.

 

looks like my 2 options are using SwitchSDTools on the PC or put switch in airplane mode and create a emunand on a seperate sd card and boot that into cfw using nxdumptool. let me know if you know of a better option.

 

I know that now maybe I wasnt clear in my post just above yours above but I was going to create a temparary emunand of my clean sysnand to and use nxdumptools to dump my games. I was just hoping there was going to be an easier way.