Hi
@mconwell, based on your problem description, it looks like you are using our on-premises Patch My PC Publisher solution to deploy your Intune apps and updates. To modify the application/update retention and assignment settings, select the Intune Apps or Intune Updates tab, and click the Intune Options button. Under the Intune Win32 Application Options header, you'll find the "Delete any previously created applications when an updated application is published" and "Delete any previously created updates when a new update is published" options. Each one of these has a "Retain up to X previously created applications/updates" option as well. There's also a "Delete the assignments from previously created applications or updates when an updated application is created" option you might want to look into. See Intune Application Creation Options Explained (https://patchmypc.com/intune-application-creation-options) for more information about using these options.
Assignments for Intune Apps or Intune Updates can be specified at the All Products level, at the vendor level, and even at the individual product level. Instead of assigning your updates to All Users or All Devices immediately, you'll probably want to configure a staged deployment to different collections with increasing delay times. See Right-Click Options Available for Updates and Applications: Manage assignments (https://patchmypc.com/custom-options-available-for-third-party-updates-and-applications) for more information about that.