Re: Ideology over mathematics
"The data in company A's backups is not indexed in any meaningful way in the current schema"
You've merged the data into B's schema. Why are you keeping backups you can't use?
"Again, the de-dupe and merge processes make automatic deletion of restored data effectively impossible."
Why is it impossible? Haven't you indexed it? On de-dupe you already deleted an entry so why should deletion of another be a problem?
Both your examples are, in fact the same: merged data sets. If the merged data set is usable it would need proper indexing and should, therefore, be possible to delete as required.