Please clarify what you mean by "Lufthansa codeshare." Were you on a LH flight operated by AC, or an AC flight operated by LH? It almost sounds to me like you were flying LH metal because LH people were concerned about recovering mile/point compensation from AC.

If operated by AC, then you should have been able to use your eUpgrade credits. Since you were dealing with LH employees instead of AC, maybe they didn't realize that the paper certs went away last year and referred to these as vouchers?

If operatred by LH, then AFAIK there is no way to upgrade with AC other than using Aeroplan miles on the *A upgrade scheme, or paying the 2000 Euro they wanted.