Please compile App1.nsi in App1 folder and install it!
       compile App2.nsi in App2 folder and install it!

And if you uninstalls any one of them that app will be completely removed. 
But it also removes the start menu links of other one too.. :-(

I was with this bug for the past two days. 

Any help will be kindly acknowledged!

Thanks and looking forward
Sincerely
Aji