Best practices with ini and PnCConf

Hi,

So I have a few things to get working (estop and charge pump) and I would like to use PnCConf for that but last time I used it (when I edited my existing config) my modbus spindle stopped working because PnCConf adds a bunch of spindle lines and gets rid of my [HALFILE = vfd.hal] line.

Is there a best practice here, I think I remember a checkbox in PnCConf to enable the spindle or something like that, maybe I need to disable that (to stop it adding a bunch of superfluous spindle lines)?

So I guess the question is, is there a way to preserve parts of the ini so they survive a PnCConf?

Thanks.
RIchard