According to answer of Matthew Scharley here:
http://gaming.stackexchange.com/a/81900 

> things won't move through unloaded pipes either so you won't get your
> materials till you go near the pipeline.

and comment of Jonathan Drain here:
http://gaming.stackexchange.com/questions/81896/how-many-chunks-do-i-need-to-keep-loaded-to-keep-quarries-working-in-buildcraft#comment120100_81900


> Everything fell out of the pipe at the point where it reached the unloaded segment.


I tried to test it and I think that the items in the pipes in the chunks that were unloaded will just stop. They will not disappear.
For new items heading through pipes into unloaded chunks, I think it is very likely that everything fell out of the pipe at the point where it reached the unloaded segment, although I do not have enough time to test it and strong evidence to prove it.