I'm not sure what you mean by "include". You are required to list all your assets and all your debts, so if you did not list your mortgage debt, you must amend to include that. Whether or not there is equity in the property, or the property is exempt has nothing to do with whether a debt is discharged or not. Your mortgage debt will be discharged assuming you get a discharge of debts. The lien against your property will remain.
Mark J. Markus, Attorney at Law
Handling exclusively bankruptcy law cases in California since 1991.
To answer your question, it is not too late to amend your Schedule D.
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As long as you did not reaffirm the debt, then it is most likely discharged. I cannot imagine that the debt was left completely off the petition. But if it was, you definitely need to amend right away.