Well, they are going to remove them from the recipes only, as requirements.
So, basically, the training manuals are becoming useless until they find another use for them.

Personally, I think it would be nice if the training manuals would reduce the chances of elemental destabilization and/or improve the rate of having HQ results on synthesis. Or, perhaps, simply slightly increase the number of items created per synthesis when the character holds the proper training manual. Anything goes as long as they don't remove them from the game.