Related to the issues here; IAMconsortium/common-definitions#165, specifically the change in common-definitions for ScenarioMIP.
Now, the components of a high-level "Emissions|*" variable (for us only "Emissions|CO2" is relevant as that's the only place where we take a sectoral split) are:
https://github.com/IAMconsortium/common-definitions/blob/90428f1099b8e6af4495dce4770418a77f93c730/definitions/variable/emissions/emissions.yaml#L14-L21
We need to add whatever is not "Emissions|AFOLU" under "Emissions|CO2|Energy and Industrial Processes".
This means: add "Emissions|CO2|Product Use" and "Emissions|CO2|Other Capture and Removal"
P.S. Also note the discussion on adding a warning, see #61.
While this seems like it would break previous behaviour, I do not expect that it would. In previous input data, these newly added variables were never reported.