If you need to change all FlashCharts in a Splunk App to JSChart, you should chekc out the following entry on
SplunkBase. There is a nice sed snippet:
find . -type f -exec sed -i 's/FlashChart/JSChart/g' {} \;
This should be executed unter /opt/splunk/etc/apps/{APPNAME]/default/data/ui/views. After a Splunk restart all your FlashCharts are gone.