I'm currently implementing iOS9 universal links for a client.
After following apple doc and some good tutorials, I succeeded to make it working almost on the first try, using a test links webpage from Safari.
But suddently, none of the test links were working anymore! I searched around during the end of the day with no answer, until this morning when I tried to open those test links from Chrome app: that worked again.
I'm very puzzled by the fact it worked perfectly yesterday, and something happened preventing Safari to present the app, displaying the website instead (No source/server code changed)
I suspect myself to have clicked on the upper right shortcut (the one with the website access), and I suspect Safari to have saved this choice. (In spit of rebooting my phone and deleting Safari cache)
Do anyone have any clue on what happened?
If Safari did really save the fact I clicked on the upper right button, is there a way to make it forget?
Okay.
St.derrick answer is very interresting, but one of his comment is even more:
As I suspected, by tapping on the top right corner of the navigation bar "mysite.com", iOS stops opening the app when you visit that URL.
To restore the initial behavior, iOS adds a header (initially hidden) on the webpage (mysite.com), with the "open app" option.
Unfortunately, I didn't find any official documentation about this behavior, which can literally drive us crazy.