The only way I know of to get modded items working mid-playthrough is by changing the meta.lsb of the unmodded savegame to the meta.lsb of a modded (new) savegame, tricking the game into thinking that the mod is actually enabled.
I'm honestly not sure if the method still works though, since we developed it back when the MetaData was in a differently named file of the savegame.
Theoretically, you should be able to start a new game with a single mod enabled and save once. This creates a save folder in Documents/Larian Studios/.../(new save game)/. Copy the meta.lsb file in there, and move to your unmodded save. Paste the meta.lsb over to replace it, and hopefully when you start up the game the mod effects take place.
Be sure to backup your saves before doing any save editing though.
Spot on! It worked perfectly. To be sure, this is what I did (in case others want to try it).
Before the following, I ripped out the modifications to the Main folder that I made earlier, so the game stopped complaining about Main being modified. To be clear, I only started experimenting with it today and did not create any new saves with the modifications to Main embedded in them (if that's the case at all).
- INSTALLED the Missing Recipes mod.
- PASTED the RootTemplates folder from the Infinite Skillbooks into ...Divinity - Original Sin\Data\Public\Fixed_and_Missing_Recipes_85e5adf9-1a66-412d-b24f-71d59331859b folder.
- ACTIVATED the Missing Recipes mod.
- STARTED a new game and saved on the beach.
- COPIED meta.lsb from this new save into the save game folder of my game in progress, overwriting the existing meta.lsb (after backing it up first, natch).
After that, I loaded my existing game in progress, and much to my delight, I could access the missing recipes AND my skillbooks did not evaporate after usage.
I wonder if you can stack multiple mods in this fashion, so long as they don't overwrite the same files or values in the Main.
Thanks for help, Rhidian and others!
