It seems when I install my app on my Android device via USB from the Godot IDE I lose my user data. How can I keep any files I've created in user:// across version updates? Thanks.
There is an option at Export > Target > Android > One Click Deploy > Clear Previous Install.
You need latest compiled version of godot to use this option.
This option works after https://github.com/godotengine/godot/commit/6cf978b7d61fa1655f13138a775acdd7fbbf39b5 this commit.
I saw that option, but doesn't it only apply to exporting as opposed to installing via USB? So while I'm developing, I'll lose my data?
One Click Deploy means that you can make an (temporary) apk file, install and run in on device with just one click with godot editor.
so, it's actually for developing and testing app, not relevant with exporting apk for distribution.
I'll mark this as correct, thanks. The IDE is just confusing IMO.
EDIT: There is a problem.. it seems that with this option set, it does not uninstall the previous version when doing a one click deploy, so it is kind of useless if that's the case.