I flipped the mentioned variables and you were right Mia's achievements are 0/2. Which is odd as my own registration shows that at some point I was at 2/2. That also means that Mia must have been visible in the phone, how could I otherwise know it was 2/2, right? So apparently something went wrong after that but I have no idea when.
Edit: I would suspect that a release level-up init after the checkup reset everything related to Mia when it shouldn't have.
Edit2: I went into my collection of saves and loaded a 3.6.0 into 3.8.1 code and Mia is there at 2/2. But loading a 3.7.0 save she is gone, so the problem happened going from 3.6.0 to 3.7.0. I don't have the level-up code from that time anymore, but you probably have.
Edit3: I narrowed it down further. I found a 3.6.1 save and Mia is gone there too. So it likely happened during update from 3.6.0 to 3.6.1. At least the level-up is the only logical place where I expect a reset of a girl to be. It makes no sense anywhere else in the game I think.
Edit4: restoring Mia will take some work. She's completely wiped. After flipping the variables in 3.8.1 checking on her finds everything gone in the phone. No access to subdermal (there was in 3.6.0) and when asking the doctor no possibility to get Mia's subdermal either.
One one hand I have checked the code and couldn't find anything that would reset Mia. On the other hand, I also have save games that have the same problems with Mia.
But for me after setting her values to True, I could go to the doctor and get her quest. Probably because I have just changed her values using teh console.
Check if you have done her "eh sperm quest". Try this in the console:
player.get_quest_state("enhanced_hl_sperm", mia)
If it returns 100
input the following in the console to reactivate her subdermal hacking:
mia.monitoring_sub_dermal_hacked = True
To get her quest back, type (only do this if: sara.get_event_seen("lab_ac1_bloodsample") returns True):
mia.add_event_seen("lab_ac1_bloodsample")
mia.add_event_seen("lab_ac1_MRI")
I have also added those lines of code to the save game patcher for 0.4.0.