When an APS Package is updated because of bug fixes, new features, and so on, the new version of the package needs to be certified as well. This re-certification process is however much simpler and is really nothing more than Odin Automation going through any changes made to ensure no bugs were introduced. We use the change-log from the packager to help us understand which changes were made, so please keep a detailed change-log when updating packages.
To certify a new version of an APS Package, sign in to the developer portal and submit the new package version along with a change-log to the support team and clarify in the submission that this is a new version of an existing, certified APS Package.