The issue of making adjustments after the payroll has been run is quite a common one, as is one way of dealing with them which is via 'roll-backs'.
You are correct in that it is your payroll software provider which will have to be contacted and asked exactly how their product will deal with this situation. From what you say in your example, it seems that an initial FPS would be created at the time the original payment is made to the employee. At the time that the adjustment is made (via a 'roll-back'), your system must be capable of recognising the + / - adjustment and reporting this on an additional FPS.
Neil is correct in that negative adjustments will not be allowed in 2012/13 (for pilot employers). However, HMRC have recently advised that they now recogise that this validation is required in their systems, however, it will only allow it from April 2013 onwards. 2012/13 negative adjustments will be via a series of 'work-arounds'.
Please do let the Forum know how your payroll software will handle the situation when you find out.
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