Thanks for your post.
This is a fairly common question actually - the problem is that the script Compare (which is used behind the scenes by Packager) generates is based on the two databases at the time the comparison was done. If you then try to run the same update on a database that's different, then it becomes unpredictable - on some occasions it may still function, but equally there are lots of differences that will cause the script to fail. So really, you need to be able to run the comparison against the target database.
Currently, Packager doesn't offer this sort of ability. The usual workaround is to investigate our Comparison SDK, and generate an application that can be deployed to your target sites to compare and update the databases directly. You can deploy your updated \"standard\" database along with your app as either a backup file or a set of scripts that the app would compare to at runtime.
There's plenty of examples here
if you do want to investigate this.
An SDK license initially allows you to deploy your app to 10 sites, but our sales team are happy to discuss discounts for \"bulk orders\"