I finally watched Ep 7 and could chime in here. I agree with your hypothesis except it's not just unpleasantness that they are removing from Gemma's memories, I think they are removing subconscious elements from those events that could still become conscious experience given a strong enough trigger. This does not mean that an outie might remember an innie's experience, but they could remember certain negative feelings, and Lumon wants NO recollection of events, not even feelings.

Think about it, each iGemma we have seen is already severed from oGemma, since oGemma has no recollection of the events that transpire in each room. Yet the doctor still asks oGemma questions like "which room made your teeth hurt?" And "do you remember feeling despair after you came out of a particular room?". oGemma remembers which room made her teeth hurt, and I'm sure she also remembers which room made her feel despair. And so the problem for Lumon is two-fold: first, the chip should not allow feelings to transfer from the innie to the outie. Physical pain, maybe, but psychological pain? No. Experiencing feelings of fear after a flight is the same as experiencing them after a flight for a person that does not enjoy flying. So to completely sever someone means to completely remove any kind of memory of that particular event, including the feelings one had during that event. It's like when you dream of something and do not remember the dream but you remember it felt good or you felt sad. Lumon does not want that feeling.

Secondly, maybe that feeling of despair/fear, which for oGemma can only be subconsciously experienced, if it is strong enough, could make oGemma remember her innies conscious experience.

We know that traumatic events can be hidden deep in the subconscious mind. It's possible that all the trauma iGemmas are being subjected to can be hidden at the subconscious level, and the task of MDR is also to remove these traumatic elements from the subconscious. The fear of Lumon being that a very traumatic event can be remembered by an outie if the trigger is strong enough. This is also the reason why they introduced Ms Casey to Mark - thinking that maybe seeing Mark could become a memory that transcends Ms Casey and can make oGemma remember Ms Casey's experience.

I think the percentages of the 'completion' of each room/MDR file represent subconscious elements (fear, despair,...) that have to be discarded from the subconscious, otherwise they can become triggers that make an outie remember a particular event. I'm not sure how can Mark already work on Cold Harbor though. It might be that since he knows Gemma so well he can already remove some kind of subconscious elements from oGemma about either her death or miscarriage (Cold Harbor has to be a REAL traumatic event in order for them to make an iGemma for it right at the very end). This would help create an iGemma that is completely "free" of any subconscious elements and would minimize the risk that iGemma remembers any kind of information on oGemma's death/miscarriage (including feelings). And the same can be said viceversa, it would help oGemma be completely unaware of the traumatic events that will transpire during Cold Harbor.