Minecraft – How to fix lighting glitches that appear on custom block models in minecraft

Given the square nature of the missing pieces, I think it's some kind of Chunk error ("chunk" being the term for any given sector in the minecraft world).

Specifically, from the notes about patch 1.2_01 on Notch's blog, emphasis mine:

• Added a temporary fix to get rid of chunk visibility errors

The last one is interesting.. The problem with chunk visibility errors was that for some reason the “dirty” flag on chunks and the list of “dirty chunks” got out of synch. There wasn’t time to try to do a proper fix today, so I just made the client check a couple of dirty chunks per frame to make sure they’re in the list.

So until we fix it proper, you might get invisible chunks, but they will fix themselves after a second or two, usually way before you even get close to them.

Here's an option. Make the enchanted books have an enchant that is applicable to the tool you want, but a high level that is possible to obtain in vanilla (i.e unbreaking 7), then after it's combined, check for any tool in a players hand with that enchant, and replace it with your 98.