I don't know how could the HR create different registrations for an employee when his adhar and telephone numbers are linked to an existing ESI and UAN (PF). Now it is their call to cancel the registrations. ESI can be cancelled only by putting left against the registration and that can be done only when you file the ECR next month. Before that you have to get coverage and for that they have to register you under the existing ESI number. But when they do that, there is a possibility that the system will reject the submission saying that 'employee with the same telephone number/ adhar number is already existing!". Then they will be stuck. In order to solve iit they may have to take the assistance of the technical team of ESIC.
In the case of PF, they can exit you even now and then again register you with the old UAN. But the UAN once created will be always be there against you and that may even be a query by the background verification team as they are more interested in such silly matters rather than important matters concerning employees.