While this may not be the situation of the OP, it may be of interest to other in a similar snafu. Doesn't always work, but it many cases it will:
If you are flying on Company A and connecting to Company B on a codeshare with A. When you check in they tell you that they cannot give you boarding pass for the Company B flight. Have them make sure that the flight number of the second flight is the codeshare flight and NOT the operating flight number.
In other words, connecting on AF to SU on an AF ticket.
AF6213 NCE-CDG and SU252 CDG-SVO will most likely come up at check-in.
If they change that to AF6213 and AF2144 then they will be able to check you in.