Since the content from the connector suddenly "appears" (and ModeShape thinks it's existing content), it is not indexed. You can rectify that by either having your connector publish events (e.g., signify the top-level node is new), or by reindexing the content using the ModeShape-specific Workspace interface that extends javax.jcr.Workspace. Either will work and will cause Lucene to index the content.
Thanks Randall. I'll give that a shot.