Export Quick Time movie drops several clips

FCEHD 3.5 user
The exported quick time movie has dropped several clips from the time line - no clips were dropped from the browser. I exported the QT Movie to external drive B because drive A was getting full (15% available) and on the prior export to ext A I had audio sync problems - about 3 frames ou of sync. The sync problem, on drive A, had just started and it went in and out over about 10% of the 34 min project. The sync problem went away when I exported to drive B but that whe 3 clips were missing from the timeline. This was the first time I used ext. drive B to store a quick time movie file.
What's causing the clips from dropping off the timeline?
Should I continue drive A as my QT export storage?

Full details about your system and the drives would be helpful.

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