I'm presuming you upgrade you're existing package in the App-V sequencer and are then adding that new package into SCCM and using the supersedence option? You can also retire the old package which will remove the files from the SCCM cache on its next deletion
cycle.
When you create a new deployment in SCCM, for you're upgraded package, it will download those package files in full (download and execute) into the SCCM cache. At this point SCCM client will attempt to Add/Mount and Publish this package; depending on whether
its targeted at a user or computer collection. It's only at this point will the App-V client determine if its an upgrade at which time if will perform a differential (delta) upgrade.
It uses RDC when you are just updating the content for an existing package i.e. modifying the dynamic configuration files.
If disk space is a limiting factor for you then you should look at using the "stream content from DP" in conjunction with the Shared Content Store.
Here is a blog by Thamim Karmin that you might find useful.