TrackX

Tracked a roof top and replaced the roof top Track X worked fine very happy with the results. Did the same again by duplicating the clip and tracking another section of the roof all was fine.

I placed the Clip and the Generator Clip (Track X) into a Compound I did the same for the other tracked clip. I did this because I was going to use a another copy of the same clip so that I could replace the sky in the clip also. After using third copy of the clip and successfully replacing the sky I then started to layer the clips so that I could use the different sections of the clip to make a finished composite clip.
To my utter frustration the tracked clips where I had replaced the roof sections were gone the replacement roof sections were in the image wells but they weren't in the canvas/Viewer screen.
Is this because they were put into CC's does that mess the whole tracking thing up?

I tried to duplicate your problem and couldn't despite making several copies of a CC. Tried it with both Simple Tracker and Track Layer.

Have you tried contacting CoreMelt support? I found Roger was very quick to reply and helped me through problems a couple of times. Hope you'll post details when you find a solution.