If the enchants generate based on your Civ level then you won't have to worry about re-getting old enchants that you've thrown out because you've outleveled them. And with random generation the chances of getting exactly some old enchant you already have had are pretty limited anyway. I think it would be neat if you have a 5% jump/speed enchant and find a 10% version and can then take the old one and put it in a blender and get X% of the enchant points that went into it back to build towards your next enchant (probably a small amount, this is more a token thing for fun than a system where you burn up one and get another one immediately). If that makes it too easy to get new enchants just balance on the back end and make higher levels get more expensive so you're still unlocking at the same rate overall but with occasional chances to rush towards something new if you burn a lot of old enchants. That way the player can feel more involved in the process without really changing up the speed of acquisition too much.
What this sort of sounds like anyway is a purchase system. I mean one could argue that's what it already is. You collect 20 enchant MacGuffin pots and trade them in for one randomly generated enchant. Sure, you're not going to the vendor and trading them off, but from a mechanics perspective that's still pretty much what is happening. All that the ability to melt down enchants will do is give you a way to 'sell old gear back to the vendor' so to speak. And adding in the potential to select between a few different enchants when you reach an unlock plateau is just giving the 'vendor' more store inventory.
Other potential ideas would be to make players actually go back to the crafting bench or Ilari stone or whatever to actually initiate the exchange of enchant points for new enchants. Gives a bit more reason to go back to town, if such a thing is desirable. You could also give the option of swapping to a new set of choices if none of those generated initially catch your fancy. This would probably allow only a single, or a limited number of swaps, and not let you reverse the decision to swap, to keep the choices interesting. You could also have a (low) random chance of generating an enchant a tier or two above what should be available at the level you're currently at, the equivalent of a rare lucky drop. Bonus standard RPG trope points for making increasing rarity colors for these enchants. (in green, blue, purple, orange...)
And this may be unrelated, but was it the enchant system that was going to add cosmetic options to spells? I may be conflating some different concepts here, but I seem to recall talk a while back about being able to change the color of spells, or something like that. Or was that crests? (Or what in the world were crests? Did that idea get dropped? Was that even a thing or am I making stuff up?) Anyway, cosmetic changes as random additions would be fun. They probably wouldn't take any points out of the enchant's overall 'budget' but just appear as random freebies from time to time.