What seems to me to have happened both in your case and that of mulan_nasil is that the interpretation of the grounds for being a Chinese Citizen have changed between when you were issued your juvenile HKID and when you got your adult one.
Article 5 of the Chinese Nationality Law as currently stated (see above) is clear. If you were born in the UK after your parents were settled there and at least one of them held British citizenship at that time (thereby giving you automatic British Citizenship at birth) then you are not a Chinese Citizen.
Someone like you in that situation born now would not have any right to a HKID card at all - they would simply be a British Citizen like all other British Citizens. However, the previous interpretation under British rule seems to have been that people of HK descent born in the UK would still have a HKID card (with right of abode). To deal with these awkward cases ImmD seems to have decided to treat you as if you were a foreigner who had acquired the Right of Abode by 7 years residency, even though obviously that's not how you did it. Under the current interpretation of the law you are not Chinese and so you lose the *** (and hence the eligibility for a HRP), and in order to retain Right of Abode you need to touch HK every 3 years. If you don't then you get downgraded to Right to Land, which is what I believe you have now.
So the not coming here for 3 years didn't actually affect your Chinese Citizenship or eligibility for the HRP (I think CTS simply made a mistake there). All it did was mean that you can't vote, you can be deported, and any kids of yours born here won't automatically get Right of Abode.
That's my interpretation anyway.