Just updated my iPhone to iOS10 and the Universal links stopped working. If I run my app in an iPhone with iOS9, or lower, the Universal Links work fine, but the are just not working at all in iOS10.
It sounds like you inadvertently deactivated Universal Links. This usually happens if you tap the bypass link in the top right corner of the screen after opening a Universal Link.
This is a per-app setting that is saved on each unique device. The setting is preserved even if you delete the app and reinstall it, so the only way to reverse this is by intentionally re-enabling Universal Link behavior for that app on your device. There are a couple of ways to do this: