You lose all Spy recon of a zone once you take it's city

[Krytor]

If you are attacking a Major and take a city, all your spy data from that zone is lost since you now own the zone. But you don't own where the enemy still exists so they all turn into ? units unless you have recon from other sources.

[Fritz1776]

Sounds like the issue is that the zone you captured is deleted and replaced with a new one under your control in the next turn. Presumably the solution is to transfer spies and recon to whatever zone(s) absorbed the old one, with penalties applied depending on relative zone sizes.

[Hazard151]

Zones without any identifying Hex Perks and/or city are also not viable targets for Strategems. Their zone is counted as 'None'.