As a restricted licence holder the buck stops with the directors. Although they may have delegated responsibility to someone else in any DVSA investigation they will be interviewed, sometimes if serious enough under caution.
If the vehicle is stopped and the missing mileage is found this would probably lead to a follow up visit to see if there are any other issues.
What the Traffic Examiner would be looking for is how quickly you spotted it and what action did you take, which from the sound of things was prompt and decisive.
I would certainly bring what has happened and what you have done to the attention of the directors if only so if something does happen its not a complete surprise.
The DVSA is looking for an operator to Monitor, Educate and Enforce, which looks like you have done in that sequence.
As for training why not see if your local DVSA office is running any new operator courses, they are usually a morning session and free, and the benefit is that it is on their records that you attended.
What drivers don’t realise is that driving for 6 hours without a break is a tachograph offence, dealt with by a trip to the magistrate court or fixed penalty and maybe also the Traffic Commissioner.
Driving for four and a half hours then ejecting your card like it’s some magic way of hiding the offence is fraud. Now that is a whole different ball game when it comes to fines, penalties and the TC’s little chat.