For the Facebook Aquila, they recently added a mechanism to align the propellers horizontally so they don't totally wreck. From their second test flight report:
Aquila's second test flight took into account the lessons we learned from our first flight. In advance of the second flight, we incorporated a number of modifications to Aquila, including:
- Adding “spoilers” to the wings, which help to increase drag and reduce lift during the landing approach
…
- Installing a horizontal propeller stopping mechanism to support a successful landing
This, unfortunately, didn't work all that well.

A few seconds before landing, the autopilot stopped the propellers as planned in order to lock them horizontally. The propellers are meant to lock in the horizontal position to avoid damaging them when touching down. In this flight, the motors all stopped, but only one propeller locked horizontally.
Still, the article says that the aircraft was in great shape aside from some minor damage that occurred during landing.