Unfortunately there was a problem in AR v8 with the service pack issued prior to the current one (051026).

If for example;
1. Your year end was Sept 30.
2. You had invoices outstanding at that time that were fully paid in October.
3. You ran year end after the October payments were applied the transaction, the transactions were deleted from the database.

If you have a backup from just prior to running the year end the lost transactions should be recoverable.