@Mike Mannella, Thanks for posting in Q&A. It sounds like you've been through quite a journey with setting up Intune and ABM for your customer's iPads. Based on the information I found, it seems that issues with syncing and checking in devices between Intune and ABM are caused that Apple needs to update something and then break the existing devices to make sure that you are on the latest setup/agreement.
Meanwhile, for iOS devices may show as "Not Contacted" in Intune. This status indicates that the devices haven't been enrolled in Intune yet. Another issue is related to switching MDM servers, which often requires a factory reset of the devices to ensure they are properly enrolled in Intune
For VPP tokens, they are used to assign and manage licenses purchased using Apple Business Manager. In general, if the VPP token is active, most time it will work well without any issue.
https://zcusa.951200.xyz/en-us/mem/intune/apps/vpp-apps-ios
Meanwhile, to ensure you manage iOS in Intune correct.ly, you can read the related links in the following link:
https://zcusa.951200.xyz/en-us/mem/intune/fundamentals/deployment-guide-platform-ios-ipados
Hope the above information can help.
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