Description of the issue:

When using the core sample drill in particular chunks (no pattern that I can see, only one 'region'/area/collection of chunks adjacent to each other). When using "/ie mineral get" an error is returned. When using "/ie mineral put " it returns that it successfully applied the mineral but does not fix the crash and using the ie 'mineral get' command still returns an error.

Crashlog:

https://gist.github.com/StormCircuit/15a1b95763c1ecccaade6a8ca38fc974

Versions & Modlist

Forge 36.1.4.
IE 4.2.4-134
(world was generated with other mods, crash occurs with just IE)

let me know if you'd like the world file.

So I setup a test environment to narrow it down: with the IE world data deleted the crashes in the previously mentioned regions stop. I tried pulling the IE world data from the original base pregen'd world and it still crashed. So the corruption or otherwise cause in the files occurred when I first created and pre-gen'd the world.

When taking the world data from a separate, presumably healthy, world of the same pregen size (4500 in properties file) the crashes disappear and minerals can be found on the previously affected regions.

Here is the old, crashing, save data:
ImmersiveEngineering-SaveData.zip

this looks like a broken mineral vein, did you check the configs? what other mods are installed(assuming the crashlog does not list all that you are using), did you remove one before the crashes started to happen?