I hope it is OK to create a new topic for this issue (it is very similar to the "Bug: AtmelStudio / VisualMicro does not parse 1.5.x Sketchbook Projects Properly" topic, except for Atmel ICE instead of the SAM-ICE).
Following the work-around for the DUE in the topic above, I created a new project (File, New, Project, C/C++, GCC C++ Executable project) and selected the SAM3X8E as the processor. I then selected "Atmel ICE" and "SWD" in the options. Compiling, uploading and running/debugging this empty project works fine.
I closed the solution and copied the INO file (for this example, I simply used the blink example from arduino), renamed it to the project name (NewBlink.ino), reopened the solution and added the INO file from the solution explorer (Visual Micro kicks in at this moment) and removed the CPP-file. Compiling seams to be fine, but upload fails! I tried out the generated upload command (...\atprogram -d cortex-m3 -v -t atmelice -i ISP program -c -f "...\NewBlink\arduino_due_x_dbg\NewBlink.hex") (long paths removed) and found the following problems:
No "NewBlink.hex" is present in the "...\NewBlink\arduino_due_x_dbg\" folder - there is a BIN and a ELF file (which is obvious from the "arm-none-eabi-objcopy" line in the build process).
"-d cortex-m3" does not seem correct, it should be "-d ATSAM3X8E"
"-i ISP" does not seem to work, "-i SWD" does.
Executing (...\atprogram -d ATSAM3X8E -v -t atmelice -i SWD program -c -f "...\NewBlink\arduino_due_x_dbg\NewBlink.elf") uploads the program and the LED blinks as it should.
After the failed upload (when using F5), the debug process (Atmel ICE) fails with the following lines:
[DEBUG] Starting execution of "program"
[DEBUG] Starting process 'C:\Program Files\Atmel\Atmel Studio 6.2\atbackend\atbackend.exe'
[DEBUG] Connecting to TCP:127.0.0.1:32885
[INFO] Connected to atmelice, fw version: 1.9
[INFO] Firmware check OK
[ERROR] Could not set device properties. Make sure you have selected correct device and interface, and that the hardware connections are correct.
So even with the Arduino DUE work-around, I am unable to use Visual Micro