As I found the hints above helpful in fixing a problem just now, I thought I'd share what worked for me in the end.

So for a BA codeshare booking via an OTA booking entirely on QR metal.

The BA PNR was fairly useless allowing basically no changes, and no visibility of seats etc. Additionally on this record, my CX FFP number was incorrectly prefixed with BA. No sign of the QR PNR

Using the hints above, I eventually managed to use Finnair MMB to fix the FFP number such that it showed the correct CX prefix. Still no sign of the QR PNR.

However, on logging into CX, I noticed the booking appeared once the the FFP number was fixed and showed a different PNR.

Bingo - this different number worked allowing seat selection via the QR site.

All a bit of a faff - but hope this helps someone down the track.