Stop ionic cap sync overwriting customer changes

I have had to make some changes to the NativeAudio plugin to get it working how I want in my app. How do I stop these changes getting removed when I add new plugins and have to run ionic cap sync?

You should not be modifying plugins like that. You should instead be making your own and applying those modifications there instead.

so fork their repo, make the change I need and then use the plugin creation process to pull it in to my project?

yep, more or less. you could just create your own plugin using the cap CLI go from there.