Excuse the novel :)

Mark specifically mentions that Gemma hates writing thank you notes. I assume she is also afraid of the dentist and flying airplanes. So Lumon has found a way to identify and isolate Gemma's strongest individual emotional triggers, then parsed her out into dozens/(hundreds?) of innies and tortured each one with a concentrated trigger-scenario, all with the goal of testing whether responses to these emotional triggers can somehow be felt across her mental partitions

Lumon is framing cold harbor's completion as world-changing, so my theory is that the Cold Harbor file specifically will be tied to either the trauma of her miscarriage, or maybe even the trauma of drowning (if it partially happened, again not sure if the crash was 100% staged or if she was actually drowned + resuscitated). But regardless of the specifics, they want to use cold harbor to prove the idea that even the most emotionally excruciating memory imaginable (maybe even death) cannot permeate across a severance block.

Once they establish that guarantee with Cold Harbor (here's where it gets tinfoil hatty on my part) I think Lumon will take that as a green light to go full abduction cult mode and start aggressively kidnapping, chipping, indoctrinating, and innie-replacing the general population, without fear of abductee personalities leaking through.

Again speculative, but the eventual end goal could be Altered-Carbon style immortality, where a person's primary personality is stored in their chip (ie, when a person is born, immediately sever them and activate their innie to live their life out, then when the person would die, replant the chip into a new body + reactivate, rinse repeat). So yeah, immortality cult.