Symptoms
Operation to update NSes when using php plugins is (or can be) asynchronously: SaveNameservers + GetNameserversStatus, but the changes in BA are commited when SaveNameservers is completed. If due to whatever reason NS update fails on the registrar side, the incorrect data is left in BA.
Cause
The issue is caused by #POA-113885 ("NSes are updated in BA control panel even when operation fails on the registrar side").