Milestones will not change the milestone preset of a player, that's intentional. I think your preset changing mid-game could lead to some unwanted changes. (e.g. you've made your own custom Pyanodons set, then Pyanodon updates the default preset and overwrites your custom changes)
However if a player goes to settings and then clicks the "Reset" button at the top, that does the same detection as when first installing Milestones, including addons.
One thing I need to double check: When a new preset is detected, Milestones prompts the player with a chat message pointing out they can use this Reset button. However I'm not sure this happens for preset addons. I should fix it if not.
I also noted that you can duplicate a milestone if you add identical milestones in several mods at once.
Probably it would be better to track this case and add only one copy of the milestone in the game.
Yeah maybe some naive de-duplication could be possible? I'm not sure it's a problem in practice, mods usually add milestones for their own items. But if there's already a conflict out there I'd be curious to know about it.
By the way, thanks for the great job with this mod
Much appreciated
Thanks!