Was the same in my save game. Don't know why or with what version this could happen. I will fix it with the save game update to 0.4.0.
If Sara has 36/36, all of Mia's values should be True. If you set them with the console, you will still miss the achievements for Mia.
I can post the codes to get those tomorrow.
I loaded a save game before the checkup and did the checkup. After that all variables were okay. So this must have been a problem of an earlier version or some specific circumstances that were not present in my save game.
In any case, I will provide an automatic fix for all of Mia's stuff with 0.4.0
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.