FYI: I wrote some similar functionality for RHQ's bundle upgrade capability. Based on that experience, I would recommend to whomever is implementing this new AS7 patch feature to review RPM's upgrade rules to see how RPM does things - this is very helpful to see the different types of conflicts you can expect and how to resolve them:
http://www.rpm.org/max-rpm/ch-rpm-upgrade.html#S2-RPM-UPGRADE-CONFIG-FILE-MAGIC
RHQ's upgrade rules ended up being very similar:
https://docs.jboss.org/author/display/RHQ/Ant+Bundles#AntBundles-UpgradeRules
Hopefully, those wikis can be helpful.