It might depend where the engine safes those files. For instance if you uninstall an Android app the OS will also delete the folder where you can create files within the internal SD card for that application (the Android/data/com.package.name folder I think). if you use the GooglePlay backend you might be able to save a file in the online profile of that user, but if you save it in the users ShaderPreferences it might get deleted on uninstall (no idea what happens on update though!).
I guess the best test is to create a beta application in GooglePlay that only you can access to see what happens in each case (but do not use your real package name because they can not be reused between apps and you wont be able to use that package name for your real game :D).