Scan paths broken after execution

Do you have have any filtering turned on?  My guess is those points are being automatically filtered out as erroneous points.

That would make sense.  I have seen that happen if a scan is set to find nominals from the model and some of the hits fall outside of the nominals tolerance.  Typically, this will stop the CMM and display an error message where it asks if you want to change the nominals tolerance. But someone may have clicked the "don't ask me again" buttons on those prompts in a way that would set the defaults to automatically delete any points for which nominals can't be found. 

That would make sense.  I have seen that happen if a scan is set to find nominals from the model and some of the hits fall outside of the nominals tolerance.  Typically, this will stop the CMM and display an error message where it asks if you want to change the nominals tolerance. But someone may have clicked the "don't ask me again" buttons on those prompts in a way that would set the defaults to automatically delete any points for which nominals can't be found.