I added a bunch of new cross-school skills and adding skillbooks for those works perfectly (=unused combinations). What doesn't work is changing the combination for an already existing skillbook.
E.g. If I change Sabotage recipe to Rogue+Ranger and then add a recpie for a new skill which is Rogue+Fire, ingame Rogue+Fire still yields the Sabotage skillbook while Rogue+Ranger is no valid recipe.
This seems to be true for all existing skillbooks. I can change the recipe via .txt ('\Data\Public\MODNAME\Stats\Generated\ItemCombos.txt') or stats editor (ItemCombos) but changes won't apply ingame.
From ItemCombos.txt
new ItemCombination "SKILLBOOK_Fire_Sabotage"
data "RecipeCategory" "Grimoire"
data "Type 1" "Category"
data "Object 1" "SkillbookRogue"
data "Transform 1" "Transform"
data "Type 2" "Category"
data "Object 2" "SkillbookRanger"
data "Transform 2" "Consume"
new ItemCombinationResult "SKILLBOOK_Fire_Sabotage_1"
data "Result 1" "SKILLBOOK_Fire_Sabotage"
data "PreviewStatsID" "SKILLBOOK_Fire_Sabotage"