Is it possible that at some point, or as a result of the update, you stopped syncing the Photos app on your iPhone with iCloud? It may be that on your PC, it had only downloaded placeholders for the photos, but not downloaded them fully, and then after the update or change, it was looking for the individual photo sources on iCloud and couldn't find them (because they're only on your phone now).
Check that your phone is syncing to iCloud and report back. Also, if you signed out of iCloud for Windows, it would have deleted the files from your PC, because that's what it does, unfortunately! When you signed back in to the app on your PC, it would have been starting from scratch as far as populating the Photos folder on your PC. I've never seen yield signs associated with files on my PC.