'andad, I don't have a clue to things BA/EC, but have been following the threads on connection protection on separate bookings between OneWorld carriers with interest given that I frequently have convoluted trips spanning different tickets, but usually on oneworld. One of the threads was on this forum and the other (one that I started) on the oneworld forum.

The latter had a post from someone having 2 bookings - CX and UL and had written to both airlines with a query similar to yours. I think both airlines had confirmed that they would indeed be protecting the connection, despite it being on separate bookings.

You might want to email both airlines as well? It would also help to call each carrier to cross-reference the PNRs, so that the other carrier 'knows' where you are connecting from.

As an aside, and not looking to rekindle the debate, I believe that the policy is to protect, and that the more established oneworld carriers (AA/BA/CX/QF) know and are well versed in this and other oneworld policies, while some of the others (MH,QR perhaps), might not be up to speed...