ESMA has updated the EMIR validations spreadsheet, which can be found here. The changes can be found on rows 47 and 68 with the first change reflecting the need to report far more trades with ISIN codes since the start of MiFID II.
The more widespread use of ISINs has caused difficulties for many in the energy and commodity market as well as the wider financial world. This article by Amir Khwaja of Clarus FT, written shortly after the start of MiFID II, looks at some of these issues. ICE has also dedicated this section of their web site to the issue.