Custom recipe's "smithing_transform" overrides base item enchantments when you add enchantments components  on results. 

Custom Recipes:

{
  "type": "minecraft:smithing_transform",
  "template": {
    "item": "minecraft:elytra"
  },
  "base": {
    "item": "minecraft:diamond_chestplate"
  },
  "addition": {
    "item": "minecraft:diamond"
  },
  "result": {
    "id": "minecraft:elytra",
    "count": 1,
    "components": {
      "max_damage": 528,
      "minecraft:enchantments": {
        "minecraft:unbreaking": 3
      },
      "minecraft:custom_data": {"material":"diamond"}
    }
  }
} 

tags/item:
trim_template.json

{"values":["minecraft:elytra"]}

tags/item/enchantable:
chest_armor.json

{"values":["minecraft:elytra"]} 

Expectation:
Custom recipe item should retain its base enchantments even you add enchantments components to the result.

Ways to replicate:
1.Download and install my datapack attached
2. Get Diamond chestplate and enchant it with any enchantments preferably prot, or mending (cuz i put unbreaking 3 on custom recipe's result for testing)
3. get elytra and diamond.
4. put it on smithing table with this orders:
     1st stot: elytra
     2nd slot(base): Enchanted diamond chestplate
     3rd slot: diamond
 
on result will only show unbreaking 3 and no protection 4