Issue solved.
Problem is that a new version of the Phonegap / Mendix template (mx-cordova-www-template) was made available thru github. This version has to be used in combination with Mendix 4.2, which is not available yet.
The right version you can find here: https://github.com/mendix/mx-cordova-www-template/tags. Use the zipfile with the name
v4.1.1.zip — Make a tag for mendix versions before 4.2.