I'm willing to say that you are going to have to reinstall all Microsoft and third-party applications that didn't make it through this upgrade.
I find this situation quite peculiar since the only time I'd seen this happen before was when 1511 came out, and it was common, but the 1607 upgrade didn't do this to anyone that I'm aware of.
The following is not meant as throwing salt in an already nasty wound, but as a cautionary tale to other readers: This is why you must get an external backup drive and take regular backups including a full system image. Even if you have system restore turned on, that could mean nothing if you have a drive crash. I tell my clients that if they want to be as close to sure as they can be to be able to get their systems back "as they were" that they need to have System Restore active and they need to do a full backup with system image at points in time where they've done enough work (e.g., installing programs, customizing their interfaces, storing passwords, etc.) that they'd cry and tear their hair out if it were necessary to do it again. Between those times it's still essential to be making user data backups.
Brian AKA Bri the Tech Guy (website in my user profile) - Windows 10 Home, 64-Bit, Version 1803, Build 17134
. . . the presumption of innocence, while essential in the legal realm, does not mean the elimination of common sense outside it. The willing suspension of disbelief has its limits, or should.
~ Ruth Marcus, November 10, 2017, in Washington Post article, Bannon is right: It’s no coincidence The Post broke the Moore story