Apple ID deleted yet iPhone still linked and can't be reactivated
So I'm trying to reactive my work iPhone after reset. It's linked to a ex employee's e-mail as the apple ID. Not a problem, I contacted her and asked her for the log in or to go to icloud and unlink it. Issue is after she left she contacted Apple and asked them to delete the apple ID as her iPad was linked at the time and she created a new personal one which her iPad was moved onto yet they left the iPhone linked to that account and now it won't recognise the apple ID even though I know it was what it was set to and when I ask to reset the password it says "apple ID not found". I then tried to register that ID and it said I couldn't as it's already being used! Basically it's a catch 22 situation because the iPhone was left linked to that now inactive apple ID which can't be accessed. The ex-employee who was registered as the owner is thankfully still happy to help but there's not much she can do either, if the iPhone was transferred to her new apple ID as well she would have unlinked it but she says it's not there so I'm at a loss what the solution is. It seems Apple should have either transferred the iPhones link to the new apple ID as well or just unlinked it before deleting the old apple ID as now there's no way of accessing it. Any help would be appreciated.
Thanks.
iPhone 5