IIRC = If I recall correctly
In DA and I think TA, if you have patched the game to where you have passive and active agents, there are no gains past "Advanced". I generally shift those 4 spies to another empire's "box". When I have "Advanced" on them all, I pull all the spies back for offensive use.
BTW, you can deploy spies on a world the instant before you invade it to lower morale, which gets you more turncoats when you use "Information Warfare" in invasions. I also use them on worlds with more than 6 pop one turn before that to trim the population I have to fight. The former does not risk those spies to nullification, but the latter does.
Oh, and as Loupdinour has posted, if you have passive spies on a race when it ceases to exists (surrenders or is conquered) you do not get them back. They become, as L coined, archaeologists. That is one very good reason to pull the passive spies out of the boxes once you achieve "Advanced".