No remap or software modification is untraceable, anyone that tells you otherwise is either misinformed or altering the truth so that the customer feels at ease with having the work carried out.
most aftermarket map switching tools cant fully return a car to standard either as they only read/write partial maps, not the entire software version.
Most ecu's also have flash counters that the dealers can see (this can also be seen by vagcom on some ecu's) but its easy to re-write these to standard flash count figures.
Someone mentioned checksum values, its true that these will change, but does anyone have the original checksum value of each and every specific standard file to compare with the suspected new 'modified' checksum? I think not.
How about cars fitted with aftermarket ECU systems such as Omex, Emerald, DTA etc... Will these all fail mot's?
It simply cant be policed, there is far too many aspects and not enough legislation let alone the equipment available to put such a rule into place, however I feel that the tuning box industry is the one being targeted with these new rules, which is only a good thing in my opinion!