We started having this problem with our 2017 S (MCU1/HW3) when the 20.44 update was installed.
Our 2018 X (MCU2/HW3) hasn't had any problems before or after 20.44 was installed - it's still accessible from the app.
What's interesting is that if I do a POWER OFF of our S, followed by a MCU restart (pressing the steering wheel thumb wheels), the app will connect for a while, before it goes offline and becomes unavailable to the app.
It could be that when the vehicle goes into sleep mode, the network connection is being dropped (even though "stay connected" has been set) and after that, the software makes no attempt to connect with the app.
I called Tesla customer support last week. While the Tesla app couldn't connect to the vehicle, the vehicle was online - Tesla was able to connect on their end and verify the vehicle was operational. I was told their technical support team would investigate and call me back. That was last week - and they haven't called back since.
Our S is scheduled next week to upgrade to the MCU2 (with a new FM/HD/XM radio tuner). When they do that, they'll have to do a new software update. Between the hardware change and the new software, I'm hoping this issue will go away.