Whenever you do a change, SAP is checking the complete material master for correctness.
The message just says that a conversion factor for alternative unit is missing.
It does not explicitly say it is related to the commodity code, but could be.
Take one of those materials that shows this error in mass processing and try it in MM02.
Change any other field and save, if you get the error message too, then it is not related to the commodity code.
If you don't get the message, then enter the new commodity code and see if you get the error.
If yes, then it might be that the commodity code itself expects a certain unit, see field BEMEH and IMPMA in table T604.
if that is the case, then you need to add the unit in MARC-EXPME along with a conversion rate and an entry in alternative units.