You have it right: external data sources can't be used as the source of study datasets... yet. The study reload feature is used to perform nightly reloads of study and specimen data from external systems. Typically, an organization writes a script or macro that exports from an external data source (SAS, a database server, a specimen management system, etc.) into a study archive (a zip file or directory containing XML and TSV files that define the data that needs to be refreshed... could be an entire study or just a subset) and then signals LabKey to reload it.

Our goal is to support reloading datasets directly from external datasources (the study archive would simply reference a query instead of a TSV file) and perhaps even support dynamic links from study into external data sources. This work is in the plan, though not currently top of the list for our current clients.

Another important aspect of external datasources if the ability to access (and modify) their data via the JavaScript, Java, R, etc. APIs. This allows building custom workflows and applications that act on external data.

Adam