There are is a collection of useful tools you might want to check out:
http://www.cs.unc.edu/~isenburg/lastools/
We had a customer with a similiar problem (it turned out that his coordinates were inappropriate), the las2shp.exe and las2las.exe helped solving the problem.
Furthermore, there is a free CheckLAS Executable on ArcGIS Online: http://www.arcgis.com/home/item.html?id=e49eaa594fb04f7f8827915345a255aa
Hope that helps!
I ran that CheckLAS when all of my points dissapeared when trying to classify points. I get the following in the log file when scanning points. Any ideas on how to resolve this problem? Is there a way to "unclassify" points? Apparently that tool messed up the records and broke my LAS file.
WARNING 1: Sum of point counts by-return (0) not equal to point-record count (12263419)
WARNING 2: 12263419 points have return-number 0
WARNING 3: 5 points have outside bound coordinates
Header: xMin = -8552418.564819336, yMin = 4900389.729583740, zMin = 458.543075562
Points: xMin = -8552418.565000000, yMin = 4900530.134000000, zMin = 458.543000000
Header: xMax = -8552091.118438721, yMax = 4900701.589935303, zMax = 530.973915100
Points: xMax = -8552091.118000001, yMax = 4900701.590000000, zMax = 530.974000000