Eric D. discovered that the layout export has the following issue...

Whenever a row on UP_LAYOUT_STRUCT refers to a missing channel -- either because the chan_id doesn't exist or because chan_id is null -- the .layout document will be missing the node that represents this row *as well as all sibling nodes that come after it*.

The cause of this issue is the SQL query that gathers channel nodes: it does a join with the UP_CHANNEL table, and therefore nodes that refer to missing channels won't be in the ResultSet.