The issue seems to only occur in Firefox.
Reproducing the issue:
Create patient with "Microcephaly"
Create new patient
Microcephaly is not present in phenotype list, however, it is shown in the gene panels, and in the JSON if you export again (before saving)
Saving the file results in microcephaly disappearing altogether
The cause appears to be that the refresh done after importing the data preserves the state of the form inputs, so NA remains checked for all predefined phenotypes even if they are properly saved upon import.
I don't have this bug in IE 11