Hey shemx, this is incredibly useful feedback, thank you. You're not missing a secret mechanic; you've identified real gaps in how the game communicates its systems.
Quick orientation: the redaction challenges are the core loop — each black bar can be contested, and your success depends on (a) picking the right exemption basis for that agency/doc type and (b) having cross-referenced enough related documents to build a case. The cross-reference board isn't just a log. Connections there actively strengthen your challenges.
The inbox going empty in Act 2 shouldn't happen. And the search not triggering anything after your clearance upgrade is something I want to look at. Can you tell me: what number were you told to search, and roughly what document mentioned it? That'll help me track down exactly where things stalled for you.