After sending an outbound X12 transaction to a trading partner, BC receives the associated 997 or 999 transaction, but does not reconcile it with the original transaction.  A 997 and 999 .sef file is associated with the 997 or 999 operation.  How to correct this?

The .sef file associated with the 997 or 999 doesn't contain DSR marks for AK1 and AK9 segments.

In an .sef file for the 997/999, these segement must have the following DSR marks:

AK1 DSR mark -> "AK1";
AK9 DSR mark -> "AK9";
AK2 DSR mark -> "AK2";
AK5 DSR mark -> "AK5";
IK5 DSR mark -> "IK5ImpTransactionSetTrailer";

Edit the .sef file with EDISIM, and add the above DSR marks to the respective segments.  After saving, upload the new .sef file to the 997 or 999 operation, and the transaction will reconcile.