Ah. I figured it out.
The same turn the PPP took place, my Last remaining ships in the system were killed by my enemy.
Before you say "well duh, if you can't see into the system you can't see populated planets", I DID have a presence in the system: a minefield.
I had previously assumed that ANY presence in a system is enough to see its current contents, and I know it to be true for ships, planets, sats, and fighters, but apparently, just having a minefield in a system isn't enough to see its contents.
I took a ship back into the system, and there it was, a newly-declared separate empire. I even got to establish diplomatic relations with the new world.
Here's an interesting question: does this newly-independent race have all the technical knowledge the original race had? So if I attack this new planet and force it to surrender, in just 2 steps (PPP and force surrender) I'll get EVERY TECHNICAL RESEARCH AREA my opponent has? I think I'll give it a try
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