Concerning the yAxis configuration in the advancedOptions, the yAxis is now configured to use an array (this was done to support the functionality of labels for percentages and handling more than 1 yAxis). Unfortunately this means that old configurations for yAxis will no longer work.
In the latest version of Apliqo (fix pack yet to be released), the yAxis configuration can be changed to yAxis0 and this will be applied correctly….
This is the way that advanced options will now save it.
Otherwise in the version you are using at the moment, to get this to work you can define your yAxis to look something like (where you wrap the object in square brackets):