[Android Auto General] xFaultx:
So Ive been easily able to reproduce the problem of AA removing the apps.

Setup (Im not 100% sure which is relevant, so including everything. Please see my setup notes below for further info on stuff I did that probably didnt change anything, but may have):

Pixel 4 XL

Android 12, January 5 2022 Security Patch

Rooted

Magisk 24.1

Google Play system update 12

ProtonAOSP Version 12.2.1

com.google.android.projection.gearhead 7.2.60124 (I do believe I was able to reproduce on 7.3.620503-release, but I needed to pee and im sick of walking out to my car)

AAAD 1.4.3

AA AIO Tweaker 5.0.2

Screen2Auto VERSION

AAStream 1.1.0.29

AAEase 0.4

SeLinuxModeChanger set to passive

Google Play Services 22.02.21

Google Play Store 29.4.13-21

How to reproduce AA removing Apps when working:

Verify Apps are listed in Android Auto under the 'Customize Launcher Button' on the phone app or are displaying in car display. They may appear under Version and Permission info, but this is irrelevant.

Force Stop Android Auto App and any screen-display apps (Only confirmed with Screen2Auto and AA Stream, so kill those two for sure)

Launch Android Auto in car - S2A and AA Stream should still be there

Open one of the display apps. I couldnt get AA Stream to work in Android 12, however it was still able to reproduce this error by just being opened. S2A was able to run and display my phones screen

Disconnect phone

Kill Android Auto app. This is the primary cause. When Step 4 of opening the display app, combined with a fresh instance of Android Auto are combined, this removes it from the list.

This can also be verified as it is NOT listed under the 'Customize launcher'

Note though they are still under the Versions at the bottom of the phone app, but are not on the launcher

Partial Fix - If you are able to reproduce the above steps, the fix is moderately easy

Kill Android Auto

Clear Storage on Android Auto

Reopen app (may need to repeat this process twice, but I have had success every time

You will need to reconfigure AA on your phone, but a portion of the permissions will be saved, saving some time (should do at a stop for safety and to not worry about speed limitations on phone)

Better Partial Fix Using Titanium Backup (UPDATED) - still testing this, but seems to have worked

Complete previous steps to make sure Android Auto shows Screen2Auto under the 'customize launcher'

Disconnect the phone from car

Make a titanium backup of the data (and application)

Next time the issue occurs, Kill Android Auto (make sure to force close, not just in the task manager)

Restore data for Android Auto using Titanium Backup

Relaunch Android Auto (I did this on the actual phone, not plugging in). I did have to force close again and reopen again to get it to work properly after restoring the data.

Verify that 'Screen2Auto' shows up under customize launcher and/or is on the main AA screen in your car

(Explanation) The reason this is better is 2 things:

Its very fast within Titanium to force close, restore data, force close, then open app. Possibly you could even make a tasker shortcut to do this. This makes it a lot less clicks, and makes it a ton faster.

It should still maintain your permissions for AA. This part I'm still verifying. The reason this is important is then you dont have to do the silly process of bouncing back and forth between your phone and car screen, giving it permission, and having to stop the vehicle just to click the 'accept' button.

Im a bit annoyed I have to keep deleting the data, and haven't seen a better solution. Please if anyone has one let me know. Possibly with my updated Titanium solution, there might even be a way to make a tasker function that Force Closes AA -> Restores Data -> Force Closes AA ->Reopens AA every time a usb connnection is made to a car. Or by looking into what is different about the data in both situations, the flag that AA is putting into the data that a DrawOverApps file was used or whatever could be investigated,

Special Notes

-I have tried using Detach3 through Magisk, the log said it installed correctly

-I used a separate app to disconnect my AA from the play store, using both methods provided. This app is on the XDA forms, but the creator asked it not be associated with circumventing AA. Think albert einstein though

-I have no idea if SeLinuxModeChanger helps, I had AA working flawlessly before moving to A12, and I had it installed previously, so reinstalled

-I have tried the above options with installing through APK, through AAAD, through AAAEase, and through AAAEase premium