Here are the steps to remove a child domain that no longer exists.
RDP – onto PDC Run – cmd at command prompt type – adsiedit.msc and then press <enter> Expand Domain – click on cn=system On the right pane, right click on the child domain you want to remove and delete
Still in ADSIEdit.msc tool
Expand Configuration – click on cn=partitions On the right pane, right click on the child domain entries you want to remove and delete.
Now at cmd – run – repadmin /syncall to replicate across your sites.
There you have it!