I'm not sure what could be causing this problem you described, as I'm seeing this for the first time to be honest. Also, you could be more specific, about the way you updated your phone.
Did you perform just an update over the old software, or you did clean install.
Also, did you change your launcher app. And what do you mean by installing "via usb cable"?
You transfered some apks to sd card, and installed them from some file browser inside the phone?
Well, this is nothing unusual, and your apps should not disappear like that.
My advise to you is to perform clean install, aka "repair" with Sony Update Service. Based on 15+ years IT experience, updating over older software never goes without problems. Not in desktop operating systems (Windows, Linux, OSX, whatever...), not in mobile operating systems, and very often not in applications.
If you're not having any super-important info in your phone, do a clean install, and then leave a feedback here.
