Evidently, MS does not support upgrading from Win7 to Win8.1 and retaining the applications. I found this out when I was considering upgrading my Win7 laptop to Win8.1. There is a table you can find that shows what carries over from one OS version to another, and MS is considering the Win7 --> Win8.1 as the same situation as XP --> Win7.
You will either have to reinstall all the apps, or if you're willing to experiment, LapLink makes a product that allows you to "migrate" from Win7 to Win8.1 -- but you would have to buy their app, reinstall Win7 (hopefully, you have a backup) and do the upgrade all over again.