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When you perform modifications in an APK file, your original signature is changed. Each developer has a unique signature that is used to sign your app before it makes it available on Google Play.
The Google Play Store always analyzes the signature provided by the developer and the signature of the app that is installed on your device. When the signatures match, Google Play displays updates for the app, if the signatures don't match, Google Play don't display updates for the app.
The only way to apply a custom patch to an app without having to make any modifications in the APK file, is to perform the patch application in root mode. If you don't have root access, this is not possible.
Read more about signing apps on Android: