Recalculate the correct rent starting from when you made this mistake, adding in the correct increases year by year.
Work out the difference between the total rent paid and the rent that should have been paid.
Reduce your tenants rent to the correct amount, less a rebate figure so that the overcharged rent is repaid in say 12 months.
Document everything; get a signed agreement from your tenant.
My inclination re RTB is to adjust the rent at your next annual registration. I wouldn't personally get into too much information with them.