@Covalt, Jonathan G, Thanks for posting in Q&A.
From your description, I know the previous enrolled device will disappear from Intune after we enroll another. Based on my researching, if the devices share the same serial number. the issue can occur. Please check if the two devices are with the same serial number.
To check the serial number, you can run the following command in command prompt:
wmic bios get serialnumber
Please check the above information and if there's any update, feel free to let us know.
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So, they're joined to Azure by AAD Connect, and then they're supposed to be pushed into Intune by SCCM co-management for now (we're planning to eliminate SCCM eventually, and when that happens we'll use GPOs to force the machines to auto-enroll).
When I was testing and discovered this, I was initiating the Intune join process via PowerShell, since SCCM was only enrolling one of the three, but now I know why that was the case, I just can't determine why it's happening.
So how I am doing this is using SCCM Co-management we put them in a group which has intune workloads in pilot and we have a device collection. If you create a pilot collection put the devices in there and if the device is in an OU that is synced with AD Connect it will place it in there. Does sound really strange. Personally instead of Enroling them through powershell you could try this method below? I personally have had no issues with this method. As long as they are both in ADConnect sync and this group it should work. Hope this helps.