Sheet Metal apparently doesn't like me making cuts to bends.
Quite possibly because of this:
Coplanar faces and face tangency between objects used in a Boolean operation is almost always a bad idea. To reduce risk of Boolean failures, take care to ensure the solid cutting the other does not share coplanar faces. In other words, make it extend so you don't see these intersection edges on the end and bottom face of Extrude006.
Nonetheless the cut works here too, and I'm very surprised!
But know that such a cut will make the part impossible to unfold. To ensure a part can be unfolded, the edges along the sheet metal should always be normal to the upper and lower faces of the sheet.
Here's how it should look like:
But this is rather out of the purview of this topic... (FYI I extruded a surface, cut it with a solid similar to your Extrude006 then used Part Offset on the result with "fill offset" option checked to create a 1mm plate. The Flatten tool is not sophisticated enough to unfold this)
OS: Ubuntu 16.04.2 LTS
Word size of OS: 64-bit
Word size of FreeCAD: 64-bit
Version: 0.16.6707 (Git)
Build type: None
Python version: 2.7.12
Qt version: 4.8.7
Coin version: 4.0.0a
OCC version: 6.8.0.oce-0.17