The same thing happened to me. Flew ARN-LHR-DOH-MNL in September. First flight on BA. Checked in all the way to MNL at ARN. Got a paper boarding pass containing all 3 segments.
Had 22 hours between flights in LHR. Passed immigration in terminal 4. Wanted to change seat on the DOH-MNL flight so I went to the check-in desk. They changed the seat but wouldn't print out new boarding passes as they were for next day. Spoke with a supervisor who couldn't explain why this is QR policy.
As I still had my BA boarding pass with all segments, I went straight to security the next day.
At the gate, during boarding, they printed out new passes.