Mariano suggests that it's possible to assign a specific measure to the line series for multi-axis charts.
"In that chart type the last measure is always the line (you can change this in the advanced properties if you want)" -http://community.jaspersoft.com/questions/843913/jasper-multi-axis-report-high-chart
Is there an example/documentation for this?
Can multiple measures be assigned as lines to the secondary axis and if so how?
You can explicitly create Y axes and assign series to specific axes.
See the attached sample report: the yAxis chart settings creates a new axis (_jrAxisIndex=1 means it's the second axis) and sets some properties for it, and SeriesProperty contributors set the series types and assings the series to the second axis.