OS reinstall breaks Android Installation

Hey Guys,
a couple months ago I reinstalled my OS (Linux Mint). I put the files into another partition and then copied them back. After that, my apps didn’t install properly anymore. I had to uninstall and then reinstall my app. I used an APK, not the Play Store. I want to switch my OS again, but I don’t want to break my app, so can anyone explain what happend and how to prevent it?