Description of the issue:

Shift+Clicking power tools into enchanting table occasionally/always? deletes the toolhead. Durability doesn't seem to make a difference but in my testing I had a few instances where the bug did not happen. Short video of problem. https://youtu.be/rtYNxTKSe9s

First discovered while playing Valhelsia 2 version 2.2.5a but went ahead and tested in a minimal instance.

Crashlog:

No crash.

Versions & Modlist - Minimal Instance

Forge-31.2.33
IE-0.15-108

They shouldn't go there in the first place, they can't be enchanted...

I have noticed a similar issue when using a jerrycan of creosote to fill a bucket. The jerrycan completely disappears when shift+click on the bucket of creosote. Only noticed it on the inventory 2x2 craft screen when the jerrycan is in the top left.
Noticed it with biodiesel as well (same positioning) but for biodiesel it shows an empty bucket as the output.

How's that a similar issue? That's a completely different issue. "Crafting a jerrycan with a bucket" is wildly different from "putting a tool into the enchanting table".
Please file a separate report for the jerrycan thing.