Contact Apple as only they can help you with this. Normally, swapping out the MDM cert requires all Apple devices to be reenrolled as the MDM profile is linked to the cert. This is all Apple device management specific and not related to Intune.
MDM Push Certificate Apple ID Change
I found an old question regarding this, but was nearly 8 years old.
We have Macs and iOS devices, but the MDM Push Certificate was setup with a personal Apple ID. We need to change this asap with minimal effect to end users. What is the best practice here? Impact?
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Jason Sandys 31,301 Reputation points Microsoft Employee
2022-08-22T20:01:13.227+00:00
6 additional answers
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Mark Jorissen 1 Reputation point
2023-07-28T13:09:31.2333333+00:00 We've updates the VPP token without problems using another Apple-ID.
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Mark Jorissen 1 Reputation point
2023-10-03T11:33:01.9666667+00:00 We have renewed the MDM Push Certificate using the same AppleID. We also have renewed the Enroll Programm Token using a different AppleID. All went well.
If you renew the MDM Push Certificate with another AppleID, then you have to re-enrol devices as far as I understand it (not tested).
The push certificate gets pushed and replaces the old one auto. No extra work required.