Potential idea here is for a placeholder block (textures forthcoming) of a ?, which can also be crafted in a grid:

-
- -
/

It would use iron ingots for the - and a / for the stairs.

When loading a quest book with invalid items or advancements, those would be marked as such with this icon. It could be crafted, placed, broken, etc, and used otherwise as a block in order to complete any tasks that use it such (detection, etc), so that the quest book is not broken with empty items.

However, it would be a permanent change: anyone who did delete a mod that was involved in the quest book would have to restore a backup of the quests after replacing it.

This is probably outside of the scope of the addon.

Could be done much simpler in retrospect. As always.