I just noticed this bug - it was fixed earlier this year:

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/b62c0d449adee39905c8e0b7cd262f22502ae67a

commit b62c0d449adee39905c8e0b7cd262f22502ae67a
Author: brucedawson <brucedawson@chromium.org>
Date: Thu Mar 30 21:35:17 2017

Get gn analyze to respect changes to vs_toolchain.py

When changing the default compiler toolchain, either when changing
_GetDesiredVsToolchainHashes() or CURRENT_DEFAULT_TOOLCHAIN_VERSION,
it is important that gn analyze knows that this means that everything
needs rebuilding. This avoids having to use the blunt-hammer of
landmines.

R=dpranke@chromium.org
BUG=  683729  ,555273

Review-Url: https://codereview.chromium.org/2780023002
Cr-Commit-Position: refs/heads/master@{#460887}

[modify] https://crrev.com/b62c0d449adee39905c8e0b7cd262f22502ae67a/tools/gn/analyzer.cc



Not obvious from the description is that once gn analyze has done its job and invoked the compiler, ninja then does its job and notices that the build command-lines have all changed (because the compiler and linker and other tools are in different directories now with a different hash) and re-runs all of the necessary build commands.