Varied chest, and double chest variants, from quark looses its texture (ie. purple and black cube textures) and cannot be opened. Breaking block does not fix issue and when placing single "bugged" chest, a double chest is placed instead. Have not tested with other wrenches from other mods.

Minecraft version: 1.10.2
Quark version: beta-40
Ender io version: 3.0.0.55 alpha

I would think that the wrench invalidates the tile entity, since it sets the rotation via state change. Furnaces change their state when they turn on/off. That would also cause invalidation of the TE, thus loosing/dropping its inventory, if it wouldn't re-set the TileEntity after the rotation.
I dunno how it works for regular chests, though, so... :/