Here's what happened when I was updated to the latest:

C:\Users\sky>gclient
Cleaning old git installation c:\src\depot_tools\git-1.9.5.chromium.6_bin
c:\src\depot_tools\git-1.9.5.chromium.6_bin\bin\bash.exe - Access is denied.
c:\src\depot_tools\git-1.9.5.chromium.6_bin\bin\msys-1.0.dll - Access is denied.
Installing git 2.7.4-64 (avg 1-2 min download) ...

Notice the access denied. That's likely because I was running a bash shell out of depot_tools.

I've seen similar errors when the windows sdk is updated and I happen to have a random process around using some file.

Given we know windows locks files that are in use before performing updates we should warn users if they have open files before trying to update files.