Thanks for the report.

Please attach the build log with the verbose and show build properties set as shown at the top of this page so we use the correct environment.

Thanks, would it be possible to ZIP and send the project over so we can investigate more easily?

A simple test example for the same configuration worked when I tried, and we will of course remove the project once the issue is resolved.

Thanks for the detail and the files.

To help us investigate further, would it be possible to follow the below steps:  files after each process has been completed?

Pre Build Capture:
Create a new project, add the settings/code as normal, then press Save All.
(This should have the indicated working intellisense at this point)
Copy the sketchname.vcxproj File, and the __vm\.sketchname.vsarduino.h to another folder and ZIP

Post Build Capture:
Build the project, and when complete, press Save All.
(This should now have the broken intellisense)
Copy the sketchname.vcxproj File, and the __vm\.sketchname.vsarduino.h to another folder and ZIP

This will let us see in more detail what is going wrong with the intellisense after the build process.

Thanks again for the detail and we can now replicate this reliably as well.

If you change the board.txt entries as shown below does the issue improve?   
I believe we only override the {runtime.tools.arm-none-eabi-gcc.path} to get the GDB Debugging working, and this can be overridden for the specific debugger as shown below

# Remove the below entry as it overrides too much of the toolchain, creating the intellisense issues
# }

# Add this: Override Just the Hardware Debugging tool to the XPack Version for the STLinkv2 (External) Debugger
tools.stlinkv2.path={runtime.tools.xpack-arm-none-eabi-gcc.path}/bin