Symptom
After exporting and importing an EDL an effect may disappear when a superimposed video track has a transition that begins before the underlying track, which also has a transition that extends beyond the superimposed track. This is best understood with screenshots.
If the original timeline looks like this:
Figure 1 Original timeline
Then after exporting an EDL and importing, it will look like this:
Figure 2 Modified timeline
Solution
Add the missing effect after reconnecting the video.