This might hopefully help someone else, as I ended up spending hours trying to chase this down.
If you have a function within your model by the same name, this will remove the value. Pretty obvious in hindsight, but nonetheless.
So, if you have something like this:
class Foobar(models.Model):
[...]
something = models.BooleanField(default=False)
[...]
def something(self):
return [some logic]
In that case, the function will override the setting above, making it "invisible" to makemigrations
.