I did see somewhere, and I can't find it again, that for that use case you would need to talk to Apple, and they can do something with the account to save it for the APN side of things.

You need to call Apple Support and provide them with an alternate Apple ID to reassign your APNS to.  They'll want the serial number and expiration date of the cert, the current Apple ID and the ID you're moving it to.  They'll also want to verify you're a legitimate employee/representative or your company.  Things like proof of employment and copies of business correspondence.

https://support.apple.com/en-us/118629

The user needs to call Apple.

The user is our IT team and we have 3 days to migrate that Apple ID. I'll ask to call one of my US colleagues.

Shared account I take it, fun. Whoever has access to the password for that account should be able to call and get anything cleared up. 

Thank you @daniel_behan and @AJPinto, solutions seem to be a mix of your advice I had a call with an Apple support and they didn't know why that account can't be transferred to a work account and suggested transferring the APN cert to a different account :)

Try contacting Apple Support; feature may depend on organization setup.