I had a similar issue. I renewed the push cert with a different Apple ID, but within the same organization, and broke the link. To fix it I re-updated/renewed the certificate with the original Apple ID and certificate. Then re-enrolled the device using the QR code, entered the network ID, and then installed the new push certificate. After doing that I opened the Meraki System Manger on the iphone and it was back in compliance and everything was fixed WITHOUT factory reset.
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