I’ve installed the latest versions of Sen2Cor (v.02.05.05) and Sen2Three (v.1.1.0). I ran some tiles through Sen2Cor and then tried running them in Sen2Three but got error messages related to the MTD_MSIL2A.xml file.
I’ve found that .xml files created by the latest version of Sen2Cor are not compatible with the requirements of Sen2Three. I know this is the case because I managed to get Sen2Three running on some old data we had lying around processed using a older version of Sen2Cor. Comparing the new and old Sen2Cor MTD_MSIL2A.xml files, there are mostly cases were “L2A_” string is missing in the newer version. However, there are also other changes.
I’ve raised the issue on Sen2Three github: