I don't like the change either. I did it because I thought I was going to change the primary substance of many ingredients and this way I could better keep track of what goes where. But it was -and still is- my intention to go back to raw ingredients in the next update.
In any case, It turns out I'm not going to change the primary substances, at least not for every ingredient. It is not needed anymore; with the addition of secondary substances the usefulness of rarer ingredients is reinstated, as these less common ingredients are the only ones to have them. It is at this point where I must deviate from the lore; some plants that had a secondary ingredient in The Witcher 1 will lack one this time around. It's unfortunate but it is a small price to pay for the sake of balance, I believe.
As for the next update, everything is coming together. The implementation of the secondary substances was more difficult than expected; the problem lies in how the same potions must coexist together in the inventory. e.g a regular Swallow potion, a Swallow with Rubedo, another with Nigredo and yet another one with Albedo. They can't be the same potion with different names, they have to be 4 different potions. After much deliberation I finally found a way to do it, so RL permitting, I should have the update ready sometime next week.