Order is reset when an item is created or deleted

A client let us know that they spent a while ordering items (using this plugin) of a custom post type, and when they trashed an item, the custom order of everything was lost.

I confirmed this by trying myself and watching the menu_order column in the wp_posts table. After trashing an item, it looks like it’s resetting the menu_order.

I also tested creating a new item and saving as draft, and the custom order is lost upon saving.

I’m doing this on a custom post type that was made with ACF. Is there a known issue?