Fraunhofer lines during an eclipse

The Fraunhofer lines are not produced by absorption in the chromosphere, they are produced by absorption in the photosphere.

The chromosphere is a hotter, optically thin region, that lies above the photosphere. During a total solar eclipse we can see the chromosphere but not the photosphere. Because the chromosphere is optically thin, any radiation produced by downward transitions, like H$alpha$, can travel freely from the Sun and is observed as emission lines.

We can only see this during an eclipse because the chromosphere emits much less light than the photosphere and so there is a contrast problem, unless you observe through a filter that picks out an emission line.