The general rule is that you check in at the airline desk for the actual flight - not your codeshare.
The problem - especially for novices - is when the issuing party of the codeshare ticket - travel agent, airline etc. - doesn't tell you what the flight number for the metal flight is.
In other words, you check in for the 'metal' flight, i.e. the one actually doing the flying. Just to clarify that.
The problem - especially for novices - is when the issuing party of the codeshare ticket - travel agent, airline etc. - doesn't tell you what the flight number for the metal flight is. Not that it's hard to find, and if staff/airlines/airports are savvy enough then they should really be able to configure their check-in procedures so that the codeshare and metal all check-in at the same set of desks.
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