These custom enchantments are not officially supported by Spigot and its item serialization. When the shopkeeper plugin loads trading recipe items with custom enchantments, and these enchantments were not yet added to the server because the plugins responsible for adding them were not yet loaded, these custom enchantments are persistently removed from the loaded items.

If the plugin adding these enchantments is not getting enabled for some reason, there is currently no way to persist the data for these enchantments (at least not when sticking to Spigot's item serialization API as we do).

However, a 'best-effort' attempt to resolve the most common incompatibilities with these custom enchantment plugins, with minimal adaptations and no guarantee for an actual futureproof resolution of these issues, might be to delay the loading of shopkeepers, to give these plugins a chance to register their custom enchantments.