The issue was that after upgrading from 6.4.2 to 7.0.0 the way we were ignoring certain properties stopped working so fields which weren't supposed to be indexed were (NEST 7 ConnectionSettings DefaultMappingFor doesn't support base class mapping anymore) .
We use a custom serializer with converters for these types when reading from Elasticsearch and it failed to deserialize these fields which meant that all fields after the first instance of the type failed to be deserialized.