${env.JBOSS_HOME} is not being resolved. I suspect it never was resolved. The reason why it worked before is that you where using it as a location to write to. This location can be anything. However, when you read, the file must exist to read from.

What I don't understand is how the arquillian.xml ever found the configuration if it was being written to something like:

/home/hudson/workspace/btny-pulls-narayana/XTS/localjunit/unit/${env.JBOSS_HOME}/standalone/configuration/standalone-xts.xml