The same people, at least Johannes Kopf and Richard Szeliski, were on both projects. So I wouldn't be surprised if there is some overlap in techniques. But Photosynth (and Microsoft's first hyperlapse research) is focused on making a 3D model using pieces of photos to recreate a scene, while the new Hyperlapse app just picks frames from a video.
If you read the detailed technology link posted elsewhere in the HN comments, you can see that this is a different manifestation of the same technology. They are calculating the camera position individually for each frame, then mapping a new (smoother) POV through the scene and re-rendering appropriately. The frames in the final video may include data from more than one source frame so that the POV can pan smoothly without cropping.
We develop a dynamic programming algorithm, inspired by dynamic-time-warping (DTW) algorithms, that selects frames from the input video that both best match a desired target speed-up and result in the smoothest possible camera motion in the resulting hyperlapse video. Once an optimal set of frames is selected, our method performs 2D video stabilization to create a smoothed camera path from which we render the resulting hyper-lapse.
