Would have to be a case of homologous recombination in response to a double strand break. For the child to not be chimeric it would have had to have occurred very shortly after fertilization making it unusual.
If it is an X linked disorder and the child is a male then it seems quite normal. Alternatively if the biological father has a deletion of that locus then the child will be affected and hemizygous which looks homozygous on sequencing . Non paternity must always be considered in genetic disorders.I am assuming that this is not a mitochondrial disorder.
Uniparental iso disomy or a de novo deletion of the gene area in the child again leading to hemizygosity