Versions:
NotEnoughItems-1.7.10-2.2.19-GTNH.jar
Electroblob's Wizardry - 1.1.6 - MC 1.7.10.jar

Issue:
Bookmark tab deletes items inserted into the Arcane Workbench on the containers it overlaps:

Without bookmark tab:

With bookmark tab:

Wizardry's GUI class in question:
https://github.com/Electroblob77/Wizardry/blob/1.7.10/src/main/java/electroblob/wizardry/client/GuiArcaneWorkbench.java

Simple way: no shift GUI to the left and use this interface INEIGUIHandler to hide NEI slots

Here's an example from tinkers: https://github.com/GTNewHorizons/TinkersConstruct/blob/master/src/main/java/tconstruct/tools/gui/CraftingStationGui.java#L275-L292

This specifically only occurs when its GUI is updated by inserting a wand, which causes it to significantly increase in width:

This problem is Electroblob's Wizard. It incorrect set GUI width when open right panel

I'd be interested in this too. It'd would be useful to know if an issue like this arises again.

There is also a method available (forestry uses it) to tell slots not to render because part of an extended GUI is there

Which part specifically needs to be changed? I'll make a PR then.