I had my first ever offloading yesterday and rather unpleasant it was too. I'd appreciate any insight into what may have happened. The story so far...

As part of a longer single-PNR itinerary (in fact a BA Hols booking) and after a lovely weekend in JER with Mrs drpabs, I flew JER-OTP via LHR. The JER-LHR leg was 0940-1050 landing at T5 and the LHR-OTP leg was 1940-0055* departing from T3. Despite my great love for the T3 CX F lounge I didn't fancy spending all day there so headed home to central London after landing at T5, rather than taking flight connections to T3. Four hours or so later I returned to LHR and had a very pleasant meal and some LP in the T3 CX F lounge. When the gate was shown I curtailed my enjoyment of the latest glass of LP and headed the short distance to the gate, whereupon I was shocked to find I had been offloaded. I was sent to another gate agent who told me that as far as BA were concerned I had not flown the JER-LHR leg so had been offloaded from the LHR-OTP leg. Upon insisting that I most certainly had flown it, she reinstated me on the flight. I asked her what this meant for subsequent flights in my itinerary, such as my return flight OTP-JER via LHR and she said she was not sure but she could try to find out, although this would take 5-10 minutes. As boarding was soon I told her not to worry about it and that I would find out myself what was going on. In MMB neither of the JER-LHR and LHR-OTP legs are shown as flown.

It looks as though I will have to spend some time calling BA/BA Holidays to sort this out - a great shame given the lovely weather in Bucharest today - so I would appreciate it if some kind, knowledgeable soul could help me understand

(i) Why the offloading happened in the first place (my suspicion is that BA's IT went in the huff because I didn't go through flight connections)
(ii) How to make sure that I don't get a nasty surprise at the gate for subsequent flights in my itinerary, including tomorrow's OTP-JER via LHR
(iii) How to get BA/BA Holidays to correctly acknowledge the flown legs JER-LHR and LHR-OTP. Whilst I do not need the TPs and avios this year for any particular reason, I am owed them for this itinerary and the TPs will help towards attaining GfL.

Apologies for the lengthy post.