I would rather create a separate stream for the different audience.
I'm not sure which version of Marketo you have - if you have Spark or Standard, you'll have to build a separate Engagement Program; if you have Select, you can just add a stream to the existing program.
If you remove leads from an Engagement Program, you lose all reporting related to those leads in the Engagement Program. Basically, it's as if they had never been nurtured.
However, if you PAUSE them (use Flow Step to change Cadence to PAUSE), then they will continue to be members of the Engagement Program, and your stats will stay intact.