What happened to my Google Chrome Install
WORKAROUND
I found that there is some kind of a Chrome glitch (as if it were the only one...) that you can read about here: https://code.google.com/p/chromium/issues/detail?id=60876
Seems a workaround (this worked for me) was to browse to the Google Chrome folder (for me it was my username/AppData/Local/Google/Chrome/Application) and delete the old version folder, along with the old_chrome.exe file. Then renaming the new_chrome.exe file back to just chrome.exe.
That seemed to fix everything, except the desktop shortcut icon, which can be easily fixed by making a new shortcut or changing the icon for the existing shortcut manually. Even WebMatrix saw my Chrome install again after this.
It was also suggested that using a registry cleaner (CCleaner is a good one), may help with some of the icon problems, but this had no impact on this situation for me.