Sanjay, if you're still having the missing apps problem (oops, I forgot- you returned your Mac), I fixed mine by following a suggestion from Linc Davis
Re: 10.11.1 update erased all apps
Linc said:
Although the problem is not the same, please follow the instructions in this support article to reset the Launch Services database. Instead of typing the shell command directed in the article, I suggest that you copy and paste it from the web page into the Terminal window. Make sure you select the whole line. One way to do that is by triple-clicking anywhere in the line.
(Back to me again)
The command is
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchSe rvices.framework/Versions/A/Support/lsregister -kill -seed
and I started Terminal by first selecting System Preferences in the Finder. I right-clicked, then Show Package Contents->Contents->MacOS-> System Preferences (thought I might be able to launch it). This process took about TEN MINUTES. When I double-clicked the black icon, Terminal started up. After I entered the command, logged out and in again, all the apps showed up.