You need it for in-town check in.

Check the terms and conditions of your online-purchase ticket, as using it at the in-town check-in "activates" it. But no, it's not considered used.

Don't know. I guess so. But I would have to ask why would you need to do that? It's as warm and inviting as a gulag.

Been there and tried it.
For a second entry to in town check in you Klook QR and/or Octopus will not open the gate.
You need to see CSR at the counter, they will check that your code/octopus has been used to access checkin but not the train and they will open the exit gate for you to enter.

I was waiting for a family member at HK station last month, but they were rather late, so during the 30 mins I saw 5 related people 'jump" the gates to the check-in area unchallenged.

The whole idea of MTR corp doing in town check-in is to encourage usage of AEx.

I know people who do in town check-in jumping the gate or follow someone and then A bus to the airport. I have followed others into the check-in are without scanning my Klook QR.

Here's what happens. Your shuttle just left and your hotel is last on the route. If you change hotels and go again, that new hotel will be last on the route. It will also be first on the route when you go back so you get to see the other 11 hotels. Take a cab especially late night. Hotel specific shuttles are OK like at Marriott Sky City though even with them sometimes a cheap taxi is a better deal.

Does AEx still operate the free shuttle buses to hotels?

Yes. See: https://www.mtr.com.hk/en/customer/s...e-service.html

Most Airport Express shuttle buses have ceased operating due to Covid-19. Only a small number as you can see from the above URL has resumed operating.

Wow, the AEx shuttle only serves 4 hotels now.

As Hong Kong opens up after Covid and as more tourists arrive, let us hope more hotels will be added to the AEx shuttle service. It was so convenient previously.

These appear to be hotel-operated shuttle bus and not that by HK MTR:

The following hotels provide shuttle bus service to and from Airport Express Hong Kong or Kowloon Station, relevant passengers may use the hotel shuttle waiting area to the shuttle bus.
https://www.mtr.com.hk/en/customer/s...e-service.html

AirPort Express on Oystwr phone app
 

Can I put the AirPort Express 3 day Iyster in the phone app?

I think the Oyster card is for the London transportation system. Hong Kong uses the Octopus card. Is your question for the Octopus phone app?

It is yes, sorry. I was typing on the tube.

I suppose you are asking whether it is possible to load the 3-day Airport Express pass onto the Octopus app and use the app instead of the actual card. I suspect the answer is no. In fact, I do not know whether it is possible to load any mtr passes onto app and use it instead of the actual card. Of course, I am not in Hong Kong and cannot test it.