How should a company deal with terminal overpayment

I'd like to ask a number of questions relating to an over payment and the way it should be dealt with by the company. Employee works for a Company for a number of years, with a salary sacrificed pension, the Employee pays normal rate tax. Employee leaves the Company part way through January, in the January pay an over payment of 3 weeks is noticed by the Employee, the Employee notifies the Company as soon as the over payment is noticed and the Company requests an amount back. Question 1: Should the amount requested be gross or net of tax/NI? The Company requests the gross amount back and it is paid. The Company informs the Employee that HMRC will issue a tax refund. Question 2: How should the company file this with HMRC? The Company uses RTI to inform HMRC that the Employee has earned less money (3 weeks) and paid less Tax (£900+). Question 3: Someone owes the Employee money, who is it and how do they go about fixing things? Over the following two years there have been several calls and letters to HMRC who state they can't do anything, and lots of emails back and forth to the Company who think they don't owe anything. HMRC believe the Employee owes £400, the Company believe the data they have sent is correct. Question 4: What should be done now to ensure the Employee is returned money owed? Question 5: How does the employee calculate how much money is owed so they can raise a claim?

Hi,
When an overpayment of wages is discovered, the money that the employee pays back should be net, this is because that is the actual money the employee was paid.
The employer will then send FPS amendments ot change the amount of money the employee was paid.
The employee isnt due a refund because by the time the FPS is amended and the money is paid back the employee never earnt that money, the company is due the refund because they have essentially paid money over to HMRC in the form of liabilities that werent due.
Thank you.