I may have this all wrong, as I don't know for sure, but I have managed to recreate sort of what you said above.
I have a file in user: on Windows, reads in to the Godot app, all is good.
Export the game to Android, run the app. No such file.
This is why I think that is.
The file only exists in user: on the Windows PC, as I put it there.
It exists in the res: directory on Android, as I exported the file as part of the project.
It doesn't exist in user: on Android, as I haven't put it there.
I don't know if there's a way of copying user: files as part of the project build, but I added a file copy as soon as the app launched and it worked as expected.
var dir = Directory.new();