It's always a good idea to remove the flexshaft before scanning. There were two main reasons for this...
1) The chuck would sometimes rotate abruptly when the scan job was started and twist the probe cable around the chuck, and...
2) It slightly reduces the overall "load" on the truck as the object is being scanned.
Reason #1 was the primary one - i.e., to prevent possible damage to the probe wire. Removing the flexshaft eliminated that problem.
See page 4 of the following Tips & Tricks:
ISSUE 9 June 2008 – Scanning Probe Techniques