Hi Jack,
there is a little warning by LASlib whenever a LASwriter ends up
writing less points than was announced in the LASheader that gets
written when the LASwriter is opened. This is expected to happen when
you clip away points and there is no need to worry because the
LASheader gets updated to the correct value when the LASwriter is
closed.
But what is probably not supposed to happen is that all your points
get clipped away. Maybe the clipping polygon does not overlap the
LIDAR points? If you send me the LAS file and the SHP file I will have
a look. But please ... LASzip compress the LAS file before sending it.
(-:
Martin @lastools