After I create Tracking Data and Apply Export, the layer I need to follow my tracking data disappears.
I bet it’s still around there somewhere. Try zooming out and looking around for layer control points. Or try checking the layers “collapse transformations” / “continuously rasterize” setting (in the timeline) (you did pre-compose, right?). Unless I’m mistaken, you should probably study up on how surfaces are “applied”. You and me both.
What is the source layer size, the comp size and the insert size?
Does the surface disappear at all in the Mocha GUI?
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This probably wont help, but…I had the same problem today.
I went back into mocha and increased the size of my tracking mask in mocha so it wasn’t so tight around my object. Earlier attempts resulted in an error message that Mocha could not track layer properly or something to that effect.
Saved it in After Effects and my top layer stopped disappearing.