I'm fairly certain that I did learned Greatest Alchemite recipe but it's not present in my savegame anymore.
Notable steps taken which may or may not affect problem appearance, in order:
Get rid of Glace for the first time
Get Nel to almost maximum relationship
Nel starts preparations for possession training
Get recipe book for Greatest Alchemite while at Alchemy around 87 and with only 1 simple Alchemite in inventory and learn it (no recipe in recipe list yet)
Sleep
Buy some Alchemite from Lucan's
Craft T2 (Greater) Alchemite until Alchemy 100, see recipe popping
Forget to craft T3 (Greatest) Alchemite to make it appear in auto crafting recipe list. Recipes requirine Greatest Alchemite still show question mark instead of it
Loot some Greatest Alchemite anywhere. See Recipes acknowledging Greatest Alchemite (no more question marks in its place). But recipe to craft said Greatest Alchemite is gone.
Savegame: https://e.pcloud.link/publink/show?code=XZfMTtZqeQKM9Gxd8FzM3TQIECCSf4yG1JX