Application update losing all data in the form of Code / Resouce path for pkg changes

We recently introduced an update on Google Play, and several users reported a problem when all of their data disappeared.

We were able to reproduce the problem once, and this was caused by:

5787 08-17 12:50:56.309 937 1030 W PackageManager: Code path for pkg : com.attidomobile.passwallet changing from /data/app/com.attidomobile.passwallet-2 to /data/app/com.attidomobile.passwallet-1 5789 08-17 12:50:56.309 937 1030 W PackageManager: Resource path for pkg : com.attidomobile.passwallet changing from /data/app/com.attidomobile.passwallet-2 to /data/app/com.attidomobile.passwallet-1 

Please note that this is not the same problem as changing the resource / code path for pkg when updating the Android application . We are ProGuarding our application, but the actual folder in which it is installed changes.

Has anyone experienced this or found out the reasons why the PackageManager is changing the code / resource path?

I found this post describing the update process for pre-installed applications, which seems to match what is happening, but our application is not a pre-installed application:

http://debuggingisfun.blogspot.co.uk/2014/09/android-3rd-party-application-as-system.html

We went through changes between versions, and no significant changes occurred; the only change in the manifest is the version number, as well as some logical changes to the code.

We have never seen this problem before with any of our previous application updates (and there have been many for the application for almost 3 years, and this update is 38).

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