If the borehole has petrophysical measurements made of the wall rocks, and these measurements are repeated along the length of the core then the two data sets correlated, one will almost universally find that the depth "of record" for a particular piece of core differs between the two methods of measurement. Which set of measurements to believe then becomes a matter of policy for the client (in an industrial setting) or of great controversy (in a context without an overriding authority. Recording that there are discrepancies, for whatever reason, retains the possibility of correcting an incorrect decision at a later date ; destroying the "incorrect" depth data makes it impossible to correct a mistake later. Any system for retaining and archiving data and core samples needs to be designed so that dissenting opinion like this can be retained.