GalCiv2 Forums
This is in ToA 2.02. If you spy on a Minor race-wide and then wipe them out, you don't get your spies back. In fact I got High espionage level on a Minor race two months after they ceased to exist.
I wrote it 2 days ago 
https://forums.galciv2.com/128951/page/15/#1966321
maybe in wrong place and in rp mode !
Loupdinour has confirmed that you don't get your spies back when a race dies, period, so this isn't a bug specific to minors. It seems you've found something entirely different in that your spies don't necessarily disappear, but rather, the slots seem to still be used-you just can't remove them. Very strange.
Wow...gaining intel after they are gone. Perhaps your passive spies are archeologists?
I submitted a bug report by email (proper way I think) just the other day to get a definitive yah/nay if loosing your passive spies is by design.
I heard back that it's been elevated to the devs for them to look at now. Hopefully soon (tm) I'll have a definitive.
I've ran into a similair problem myself. In my case, I got further intel on the Drengin after they had surrendered to another civ.
In DA I occassionally can see the spy symbol on a planet that no longer has a spy. I also sometimes have my spies negated but aren't told about it, I'm always the last to know.
Same in TA 2.02, there is a shift in time before you are told about spies loss, E=MC² problem somewhere !
I think that's due to the AI going when you are going (at least on the planetary level as well as picking where it's ships are going to go after you hit the End Turn button). So technically, during your turn the AI nullifies/places the spies. It isn't until your next turn that you'll get the message that they have been nullified/placed.
No, there's a definite one-turn delay. If you're on top of it, you can remove enemy spies before you are told they are there. Similarly, if you place a spy, it cannot be removed the first turn. They will always last until at least the second turn, which means the AI suffers a similar time delay.
Theoretically, a sharp player could place their spies, remove them the next turn, place them the turn after, remove, ad nauseum and never lose a spy and keep an AIs buildings disabled half the time. You could move spies from planet to planet and get the same effect with the spies in use each turn. Moving from tile to tile doesn't work, however.
I had the same problem. I had 4 spies on the Yor, and then they were wiped out by the Thalans, and I lost my spies, no refun, no passing go. 
It's a known bug now, they should have it fixed in the next patch.
Your spies are too good. They looked so much like robots, the Thalans killed your spies as well. Move your "competency skill" slider under your espionage tab to the lowest setting. That way, next time they spy on the Yor, instead of looking like this:
They will now look like this:
Hope that helps!
Oh - *there's* my agent problem - My competency slider seems to be pegged on the left hand side!
No, wait . . . hey, this says "Player Competency"?!?!? What are they trying to tell me here!!!!!
{G} - Jonnan
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