I have a noob question: We have a limited number of Foundry slots. So once a mission is published, and we erase the project in the editor to work on newer missions, does that original mission stay out there for the community to play (we just can't modify it anymore) or does it get deleted?

If you delete it, it gets deleted. Maybe after the F2P transition they'll add the ability to buy more Foundry slots.

It'd be worth the investment to me. I have many stories I'd like to publish, but I hate having to scrap ones I've already written. It'd be one thing if my old mission sat on the server for months and no one played it, but I still don't want to have to pick and choose what stays and what goes.