When the code to update based on ZIP went to look up the child fragments, it explicitly used the paths provided in the ZIP. This meant that we could never detect omissions because there'd never be a scenario where a child fragment would return but not exist in the ZIP. To fix this, the query should be using withLeadingPath instead of withPaths.

Uploaded a ZIP that omitted a file and saw the deleteFile get called (by placing debugging output in the code).