@DaveK Thanks for posting in our Q&A. From your description, did you mean that the retire action uninstalled the apps that you deployed via intune? If there is anything misunderstanding, please correct me.
In our official article, it shows that the app will not remove when it is configured to not be uninstalled on device removal.
https://learn.microsoft.com/en-us/mem/intune/remote-actions/devices-wipe#ios
Honestly, I tried the retire action in my iOS BYOD device and set the 'Uninstall on device removal' to No, it doesn't uninstall the apps managed by intune.
Given this situation, it is needed to do the log analysis to find the root cause why the app is uninstalled. With Q&A limitation, it is better to create an online support ticket to get more effective help. Here is the support link:
https://learn.microsoft.com/en-us/mem/get-support
Hope it will help.
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