I've never used Mocha before, and it seems based on videos I've seen that it's great for tracking, but I wanted to ask here before I start watching an hour or two of tutorials to see if it will do what I need. I shot some handheld footage of the downtown area in my city just to do some compositing practice, and I need to duplicate the layer, and in the top layer leave only one the buildings. Keyframing a mask would take forever, so that's why I want to learn Mocha, but the problem is that I panned a few times, so the building goes in and out of frame.
Would Mocha (the AE CS6 bundled version) work in this situation, or is Mocha only for tracking objects that are present during the whole sequence?
Go to the Mocha website and look at the Mocha for AE tutorials. Mocha can easily handle your shot if it is as you described.