Moneysoft - query re defunkt employee from 2yrs ago

In 2009-10 an employee was a leaver and a P45 was logged manually on HMRC site, so has not appeared in HMRC records for 2010-11 or 2011-2012, correctly.

The employee leaver date did not get entered in Moneysoft in 2009-10. 

So the record still appeared at 5 April 2011 in Moneysoft records.  A manual P35 was submitted to HMRC without him on the list (correctly)

Now I am at the point of submitting the P35 for 5 April 2012 via Moneysoft (not manually).  I cannot remove this defunkt employee from the current M-Soft records - will it throw a spanner in the works with HMRC as they have no record of him