I would recommend that when you do a clean install you not have any apps available on the web installed. Than after you install the OS you can download BlackBerry AppWorld at mobile.blackBerry.com and begin loading the newest version of everything, including BlackBerry Protect.
Only exceptions would be BlackBerry Maps and Password Keeper since they are impossible or hard to find OTA.
This way your not putting old apps on your fresh new install and then updating them.
"Windows UPGRADE" mean anything to you?