I finally got this sorted after nearly three hours of phone calls with ET and A3. ET was helpful though some agents were clearly not very knowledgeable.

At first I was told I could change my ticket to BER-CPT via LHR or FRA with the longhaul legs on ET and was put on a waitlist with confirmation expected within minutes. Nothing was coming through, so I called again and another ET agent checked with the reservations department and supervisors confirming 100% that the departure point cannot be changed on award tickets from other airlines even in such cases. I tried quoting EC261 but I didn't have much luck. I decided to book a last-minute separate flight from BER to FRA (since the train was even more expensive) just to be done with it. A lot of hassle and I wish it hadn’t happened since it cost me the whole evening researching options.