There are 6 unique codex entries in the Locations section from Flashpoints. 4 are accessible to all players regardless of class or faction and 2 are faction specific.
Colicoid Creation Nest is obtained near a proximity map trigger during "[FLASHPOINT] Colicoid War Game" mission.
Codex type: Locations | Faction: Both | Class: All
Associated Achievement: None
Hammer Station is obtained near a proximity map trigger during "[FLASHPOINT] Hammer Station" mission.
Codex type: Locations | Faction: Both | Class: All
Associated Achievement: None
Maelstrom Prison is obtained from completing "Disrupting Defenses" bonus mission during "[FLASHPOINT] Maelstrom Prison" mission.
Codex type: Locations | Faction: Republic | Class: All
Associated Achievement: None
Shrine of Silence is obtained near a proximity map trigger during "[FLASHPOINT] Shrine of Silence" mission.
Codex type: Locations | Faction: Both | Class: All
Associated Achievement: None
Temple of the Ancients is obtained near a proximity map trigger during "[FLASHPOINT] Legacy of the Rakata" mission.
Codex type: Locations | Faction: Both | Class: All
Associated Achievement: None
The Foundry is obtained from completing "Forgotten Technology" bonus mission during "[FLASHPOINT] The Foundry" mission.
Codex type: Locations | Faction: Imperial | Class: All
Associated Achievement: None