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When new version of an app gets published to Intune it would be nice if had option to update the dependency and not just copy the existing dependency.
The checkbox that is in the Intune options should ensure that dependencies are kept up to date if both apps are managed by Patch My PC. If only one of them is managed, then all we can do is update the Intune application that we managed.
Do you have a specific scenario that is not working?