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ha i just independently found this same issue. useeior::checkNamesandOrdering() called via writeModeltoXLSX() throws an error and I confirm the problem is exactly as you state. This will become a problem for using the model via the API as well as via Excel if one simply used the index (row number) to get flow metadata.
see USEPA/useeior#244.
I believe the only consequence of this is that the flows tab in the excel file has 3 flows that do not exist in the model matrices.
In this case, these three flows appear in the FBS for CAP_HAP but only for F01000 sector.
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