If you are installing the APK on the devices via Package then you will need a Pre-Install script within your Package that Uninstalls the App before the new version of the APK is installed. This will have the negative effect of wiping out any permissions and restoring the prompts that may have been manually granted in the past as well as wiping out any App Cache or App Data that may exist on the device but will have the positive effect of allowing you to cleanly install the new APK version. In the future you should be able to do a direct upgrade to say version 3.0 provided that you use the same SOTI Package but just update the APK contained within and increment the Package version number accordingly. 

Matt,

Thank you for the information, yes, the APK is deployed via package but I did not add a pre-installation script. I'm OK with losing permissions and cached data. This should resolve my issue going forward, but my current issue is still open. About 75% of my phones have an uninstalled version 1.0 and a failed installation of version 2.0. Any suggestions on how to resolve this?

Hi John, 

How many devices are we talking about and what other configurations/profiles do you have on the devices?