For some reason when you upload a new APK without immediately clicking "publish" (you probably clicked save draft the first time), Google thinks you want to publish BOTH apk at the same time.
This is usually needed when you have multiple APK for different configuration (say: a version for android 2.x and another for 3+ or a version for tablet and another for handset etc...)
However in your case you are just uploading an upgrade and you want it to replace your previous APK.
To solve:
- Click on the Switch to Advanced Mode on the top right
- Click on Action -> Move on the OLD APK and choose "Deactivate"
- The error should go away and you should see your OLD apk in "OTHER APKS" and the new one ready to be published.
- Just click Publish to make your change effective and wait for them to propagate.
The Google warning is missleading.
Hope this clarify it.