Yes, you can replace already existing app with Flutter app but you need to take care of few points to be able to do this.
Please take care of following things:
The package name must be identical with the old application. Please take a look into Manifest file of old app and replace the package name in new application AndroidManifest.xml file with the package name from old application.
Now take care of the versionCode and versionName, this info can be retrieved from AndroidManifest file of old application and upgrade it in Flutter's pubspec.yaml file with version attribute as it is must to keep it greater than previously released application. This attribute has the form of 0.1.1+3 where 0.1.1 corresponds to versionName and 3 (the number after + sign) to versionCode.
Here's the crucial part, the keystore file used to sign New Flutter's version must be the same used to sign the Android's native release.
If you follow all these steps then you can update the new version of the application irrespective of the programming framework you are using i.e Kotlin, Flutter, React Native or any other technology.