Just a quick update, I've currently received no response at all from Southeastern, having returned the letter to them as requested. I don't know whether that's because it is a lengthy process to deal with, or whether I can deal with this as a closed matter. They haven't been very helpful, considering this all concerns my personal information.
TfL have also been unhelpful, and have failed to deliver me an Oyster Journey History (on my second attempt at getting one!) but I still have a receipt of my Oyster transactions to prove I travelled legally on the day in question.
Once again, I'd like to thank the helpful people here who generally managed to point me in the right direction in terms of a course of action