I have a done a bit in motion, and with large projects (either a lot of effects, big HD, long project) I have often found a video disappearing when making a change. The really annoying thing is that when I export it the video is still gone.
My Solution:
Break up the project into smaller chunks. Or if you are doing multiple layers of effects, turn off all but the first layer and export. Then bring the newly effected file back into Motion, and add more effects.
If you are only doing time remapping you probably can’t turn off other effects, but you can cut it into smaller chunks (on one project I was working with 10-15 second clips.
I hope this helps
-Proby