I don't know how HR could create different registrations for an employee when their Aadhar and telephone numbers are linked to an existing ESI and UAN (PF). Now it is their call to cancel the registrations. ESI can be canceled only by marking a 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. However, when they do that, there is a possibility that the system will reject the submission, stating that "an employee with the same telephone number/Aadhar number already exists!" Then they will be stuck. To solve it, they may need to seek assistance from the technical team of ESIC.
In the case of PF, they can exit you even now and then register you again with the old UAN. However, the UAN, once created, will always be associated with you, and that may even raise a query by the background verification team as they tend to focus on such minor matters rather than important issues concerning employees.