I'm not familiar with Sage processes but there is a more general payroll point.
The employee must not be given an amended P45 unless you get the original one back from them. Under no circumstances should an employee ever be given two P45s relating to leaving the same employment.
I have done this before, I submitted a P45 to the wrong employee this can be amended on Sage Payroll. Do you have Sage technical support? Tom is correct you must get the employee to bring you the original P45 back, you can hold the holiday pay until they do.
Take a look at this link - http://www.hmrc.gov.uk/employers/p45-employee-leaves.htm#5
This happened to me once, I had to make a payment of holiday pay to someone who I'd already produced a P45 for and I had to write to HMRC. I had however already submitted their P45 to HMRC.