AI Limit has a total of 4 Hereditary Resonances that you can collect throughout the game. These are used to upgrade Main Seals to the highest level, with a maximum of 4 being obtainable per playthrough, so that is the maximum number of Main Seals you can fully upgrade per playthrough. One of the Hereditary Resonances is missable, but the rest can still be obtained after defeating the final boss if you choose not to go into New Game+.
Obtaining at least 1 Hereditary Resonance is required for the trophy/achievement 
Weaver – enhance any Main Seal to the maximum level.
Hereditary Resonance
Below are listed in the order they can be obtained as you progress through game.
Hereditary Resonance #1 – Branch: Sunken City Underground – Underground Parish > Living Pond
*MISSABLE*
Note this is the only Hereditary Resonance that can be missed during a playthrough. To obtain it you first need to finish Stone’s entire questline and earn the trophy/achievement Friends Reunited. You can then go back to a Branch to refresh the area then come back into the room where you last interacted with Stone. There will be a group of NPCs standing around a coffin. Speak to the one in the middle and exhaust his dialogue to receive a Hereditary Resonance.
Hereditary Resonance #2 – After defeating the main story boss Eunomia, the Resplendent Bishop you can return to Millaire at the Temporary Campsite. After speaking with her and handing her the Vessel Remains you can purchase one from him for 10 Adaptive Fragments (once per playthrough).
Hereditary Resonance #3 – Branch: Hagios Patir – Upper Level > Evolving Palace
Follow the main path until you drop down the ledges into the large room. Follow the path around to the left to reach the platform where the three ranged enemies are standing. The Resonance is inside the cube in the corner.
Hereditary Resonance #4 – Obtained automatically after defeating the Seraphim Absolver main story boss at the end of Branch Hagios Patir – Upper Level > Evolving Palace.
For all other collectible types check out the AI Limit Collectible Guide.
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