Basically, after doing a git pull on master and running gclient sync, I am left with a broken chromium tree, where most of the directories and files in the tree are gone.

I am starting with a clean master branch that is tracking origin/master

c:\src\chromium\src>git checkout master
Branch master set up to track remote branch master from origin.
Switched to a new branch 'master'

c:\src\chromium\src>git branch -vv
* master 4e18c94 [origin/master] Reporting: Cap number of reports in cache.
  oop    c028830 [origin/master: ahead 5, behind 204] fixes
  run    887d569 [origin/master: ahead 981, behind 590745] Merge pull request #965 from davidben/format-attr

c:\src\chromium\src>git pull
Already up-to-date.

c:\src\chromium\src>git status
On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working tree clean

c:\src\chromium\src>gclient sync
Syncing projects:  99% (142/143) src/third_party/skia
[0:01:58] Still working on:
[0:01:58]   src/third_party/googletest/src

[0:02:08] Still working on:
[0:02:08]   src/third_party/googletest/src

[0:02:18] Still working on:
[0:02:18]   src/third_party/googletest/src

[0:02:28] Still working on:
[0:02:28]   src/third_party/googletest/src

[0:02:38] Still working on:
[0:02:38]   src/third_party/googletest/src

[0:02:48] Still working on:
[0:02:48]   src/third_party/googletest/src

[0:02:58] Still working on:
[0:02:58]   src/third_party/googletest/src

[0:03:08] Still working on:
[0:03:08]   src/third_party/googletest/src

[0:03:18] Still working on:
[0:03:18]   src/third_party/googletest/src

[0:03:28] Still working on:
[0:03:28]   src/third_party/googletest/src

[0:03:38] Still working on:
[0:03:38]   src/third_party/googletest/src

[0:03:48] Still working on:
[0:03:48]   src/third_party/googletest/src

[0:03:58] Still working on:
[0:03:58]   src/third_party/googletest/src

[0:04:08] Still working on:
[0:04:08]   src/third_party/googletest/src

[0:04:18] Still working on:
[0:04:18]   src/third_party/googletest/src

[0:04:28] Still working on:
[0:04:28]   src/third_party/googletest/src

[0:04:38] Still working on:
[0:04:38]   src/third_party/googletest/src

[0:04:48] Still working on:
[0:04:48]   src/third_party/googletest/src

[0:04:58] Still working on:
[0:04:58]   src/third_party/googletest/src

[0:05:08] Still working on:
[0:05:08]   src/third_party/googletest/src

[0:05:18] Still working on:
[0:05:18]   src/third_party/googletest/src

[0:05:28] Still working on:
[0:05:28]   src/third_party/googletest/src

[0:05:38] Still working on:
[0:05:38]   src/third_party/googletest/src

[0:05:48] Still working on:
[0:05:48]   src/third_party/googletest/src

[0:05:58] Still working on:
[0:05:58]   src/third_party/googletest/src

[0:06:08] Still working on:
[0:06:08]   src/third_party/googletest/src

[0:06:18] Still working on:
[0:06:18]   src/third_party/googletest/src

[0:06:28] Still working on:
[0:06:28]   src/third_party/googletest/src

[0:06:38] Still working on:
[0:06:38]   src/third_party/googletest/src

[0:06:48] Still working on:
[0:06:48]   src/third_party/googletest/src

[0:06:58] Still working on:
[0:06:58]   src/third_party/googletest/src

[0:07:08] Still working on:
[0:07:08]   src/third_party/googletest/src

[0:07:18] Still working on:
[0:07:18]   src/third_party/googletest/src

[0:07:28] Still working on:
[0:07:28]   src/third_party/googletest/src

[0:07:38] Still working on:
[0:07:38]   src/third_party/googletest/src

[0:07:45] Still working on:
[0:07:45]   src/third_party/googletest/src
Syncing projects: 100% (143/143), done.

________ running 'c:\src\depot_tools\python276_bin\python.exe src/build/landmines.py' in 'c:\src\chromium'
c:\src\depot_tools\python276_bin\python.exe: can't open file 'src/build/landmines.py': [Errno 2] No such file or directory
Error: Command 'c:\\src\\depot_tools\\python276_bin\\python.exe src/build/landmines.py' returned non-zero exit status 2 in c:\src\chromium

After this is done, my remote points to a github repository for googletest, and my branches are destroyed:

c:\src\chromium\src>git branch -vv
* master 43359642 [origin/master: behind 134] Merge pull request #616 from anuragsoni/documentation/fix-readme-for-googletest
  oop    c028830 [origin/master: ahead 590546, behind 981] fixes
  run    887d569 [origin/master] Merge pull request #965 from davidben/format-attr

c:\src\chromium\src>git remote -v
origin  https://chromium.googlesource.com/external/github.com/google/googletest.git (fetch)
origin  https://chromium.googlesource.com/external/github.com/google/googletest.git (push)