I
think I know what your question is. I'm having to fill in a lot of blanks.
When you load clips into the media room, and put them into the timeline, the files themselves aren't moved. All PD has are pointers to the files' locations. They aren't "in" PD.
If your clips aren't on your hard drive, then whatever external device they are on has to be continuously available.
This might not be causing your problem, but from the way you phrased your question I thought you might not understand this.
As for why the rendering isn't completing, if the files are on you hard drive I don't have an answer readily to hand.
Jerry Schwartz