When you refer to “the other one is predefined as DD.MM.YYYY” are you referring to the “Last Updated” date field? The “Last Updated” date is determined by the Endnote software and the Endnote developers made the “Last Updated” field inaccessible to users so users cannot change the data within the software program.
It might be possible, however, to manipulate the exported Medline text by using either MS Excel or Word to find and replace the periods with slashes prior to importing the data into Endnote.