This is not always just because a discrepancy has occured, but yes this may be the reason. More than likely it will be because the vehicle is now in the hands of a franchised dealer who wants to sell it.
Most large dealer groups do not want to risk having their reputation sullied by selling a vehicle that could have a mileage discrepancy, therefore, as standard when a vehicle is taken in they will carry out a mileage investigation. The letter you have recieved is a standard letter that is sent out to help build a picture of a cars history to ensure it has not been clocked, through these letters, dealer submissions, DVLA data and other sources the HPI "NMR" database now has over 125 million records.
Under consumer law if a dealer wants to sell a vehicle as "warranted" mileage they must show proof, a mileage investigation is such proof. If a dealer is selling a vehicle as guaranteed mileage, always ask to see if an investigation has been completed, particularly if the vehicle is older with a few owners, sadly the move to digital odometers has not stopped clocking and it is still a major problem for the industry.
As an aside, Mileage checks also come as a standard part of the HPI consumer check these days
1 in 3 Cars has a hidden history. Check it before you buy it.