It looks like when a block of documents is indexed, child documents get no _version_ field. This means (among other potential issues) that a delete-by-query that is reordered will cause matching child documents to be deleted. DBQ normally prevents deleting newer docs by including a restriction on _version_, which doesn't work for anything lacking that field. Re-ordered delete-by-term of any child docs would also be affected (although it should be a much rarer issue.)
The leading candidate for a fix is to use the exact same _version_ for all child docs.