I'm sorry you're experiencing this, but the problem is the way android works. Sometimes it updates the app again when you install it, sometimes not. That's why we recommend that when you are going to install the new version on your device, you back up your saves, uninstall the previous version and install the new one. Unfortunately we have no control over the behavior of android on each device.
That's not exactly how this works... but I'm not about to argue about it. It really is an APK side, not a device side, thing that prompts the APK to update instead of fresh install. As for backing up the save, it was never deleted. The fact that the APK prompts the creation of all new folders and files is where the disconnect is. Literally your game used to properly update until some time last year I wanna say, when you started adding in new features and overhauls. It's why I made this post (again) bringing it up and asking if anyone else has found a fix because I'm tired of trying to fix it myself when hidden mobile files are annoying to get. If it was PC, like the Windows files, then it would be relatively easy. But when you even use a file browser app and can't find the right file to put in the right folder... or of you do and it just fundamentally breaks because the save doesn't update when transferred (like in this case)... regardless, as I said I was hoping someone else had a fix, but it's kinda harsh seeing the dev actually respond and say they have no control over it as if someone else makes the APK for them lol