When I enter a new value for Initial Step size in the focuser sub-module, the new value does not persist after a Start & Stop of INDI.
It's likely that this is not the only example of non-persistence I may have. Is there a general fix for this? I would rather not delete the settings file, but I'll accept it as an option. Otherwise how can I manually edit the value stored?

Should persist once you complete one autofocus run IIRC.