If you end up having employees in your system with duplicate NI Numbers, and the employees end up with benefits on both 'profiles'. This will mean that the employee in questions would end up with two P11Ds when you produce them - that might be exactly what you want, but if you only want one, the system can merge all of the benefits onto a single employer.
This guide will step you through the process.
Go to the 'Setup Filter' option:
Then set a filter based on 'All employees with benefits and expenses and duplicate NINO' and click "Filter":
You will be presented with a list of all the employees in the system with duplicate NI Numbers who have a benefit.
Then select the entry that you want to become the main record, and go to Tools>Recalculate benefits>This employee. You should be presented a screen like this:
Click "Yes", and you will see a screen like this:
Click "Yes", and all the benefits will now be on the one employee - the other employee will still exist in the system, but with no benefits.