This is probably more of a general issue: when *master* is set to use biblatex, and a child hasn't been changed to use biblatex as well but uses, for example, natbib, two inconsistencies can happen: 1) when child contains "Insert>...>Bibliography", it will have \bibliographystyle and \bibliography commands, but will add the correct \addbibresource to the master. The solution would be to automatically switch the child to biblatex or at least warn the users of this inconsistency on their side. 2) child can have commands like \citeyearpar that will not be recognized by biblatex when the master document is compiled.
I'm actually wondering if there's really need for child documents to have their own Document>Settings (their own preamble), independent of the master document's settings. What are your thoughts?