There is currently a glitch in the mod where you can duplicate items/accidentaly destroy them if you have an animated structure containing a storage sub-structure (e.g. your typical drawer) and open the storage GUI in the middle of an animation.

Steps to reproduce:
1- Create a storage block, save it to a recipe (set it to storage mode)
2- Create anything using chisel (e.g. drawer), place storage structure on it, save everything to an advanced recipe (keep structures)
3- Create an animation for your structure, set it to last 3 or 5 seconds or so. Place the structure on the world.
4-Place any items inside the storage. Now right click the structure to animate it, and WHILE animating, right click the storage block.
5-Do not close the gui until you see the animation finish in the back. Once it finishes, and still keeping the gui open, take the items into your inventory.
6-Close the GUI.
7-Right click the storage again. The items will still be there as if you hadn't taken them, so now you have two of each

I suspect this is caused because the inventory state isn't updated when exiting the GUI. I lost a couple of items while making a disk rack/cupboard by right clicking my drawers while animating. Put something in after animation finished and it got replaced by the empty inventory again, thus destroying it

Finally got around to fix it ... unfortunately it's a little more complicated ... will continue to work on it next week. Sorry for not responding earlier.

Is fixed in the newest pre-release. Thank you very much for reporting this serious issue! Sorry that it took so long.