Switching between publishing to iOS and Android will wipe out the icons, or at least the ones that don't exist for that platform. We've been requesting a way around that for years now.
In the meantime, there are some things you can do to make life easier. Have two FLAs, one for iOS and one for Android. They can both use all the same external files (including SWCs that have been added in the AS3 settings), so the main FLA itself need not be too huge. If all of your work is inside one FLA, the second one I'm suggesting would be big. And I know that if you did a lot of work on the FLA you would have to carry over the work to the other version. But hopefully a lot of the changes you're making are in Class files, which would be shared between the two FLAs.
In any case, if you could work that way there are advantages. You would only need to add the splash screens to the iOS FLA, you only need add platform specific ANEs to corresponding FLA. And, your list of icons would survive each time.
If that seems like too much trouble there's another thing you can do. After choosing the icons for Android, open the app-descriptor XML file and copy the list of icon tags into another text file. Do the same for iOS, and copy those ones to another file. When you want to publish and find that all your icons are gone, copy and paste them back into the XML file. Then in Animate, instead of opening the publishing settings and doing a publish there, use File/Publish. Doing it that way should leave the XML file intact, with the long list of icons still there.
Thank you very much Colin,
in the meantime I have found a better solution:
Icon location is never saved with AIR profile
1 - Icons and exported SWF must be in a subfolder of location where main FLA or XFL are stored.
2 - Before setting icons, after setting swf name, publish briefly, so that -app.xml file is created before setting icons
Icons (and other options) get wiped when switching between Android and iOS
This is because you share the same [swf name]-app.xml between the 2 AIR export profiles. What you have to do in order to retain separate AIR settings using the same fla is as follows:
1 - create 2 publish profiles, one for AIR Android and one for AIR iOS
2 - make sure the exported swf has a different name for each profile (this is vital, since -app.xml file is saved with the name of the swf as prefix). Doing this you will have 2 separate manifest files.
3 - This is also vital, after you correctly filled up each manifest, make the -app.xml file read only, so that AIR exporter will not mess with it.
Doing like this, each profile will retain it's own AIR settings, including icons, ANEs, etc. It's all related to the *******' exported swf name.
I wish Adobe, in a decade, made a final guide for these little perks, updated to each AIR version, in order to save us a lot of valuable time (since we pay a monthly fee now we may well expect this to happen).
I hope this helped.