I've tested with the following wrenches, and found that when used on a dark utilities chest, they reset the inventory, deleting everything inside of it:

• Ender IO's
• Forestry's
• IndustrialCraft's
• Redstone Arsenal's
• Refined Storage's

Thanks for reporting this bug. I've since removed chests completely, due to a few really big bugs with them. They will likely see a return some time in 1.12. I have played around with a new system which doesn't have this issue. It's just not ready to implement yet.