When a discharge medication is marked as "NOT PERFORMED" in Bonnie the entityRelationship/substanceAdministration is negated rather than the act. This is inconsistent with similar templates like medication administration where the act is negated rather than the related substance administration.

In attached examples see STK-2_205.xml for an example of a negated discharge medication entry and STK-4_405.xml for an example of a negated medication administration entry.

From the latest HL7 IG:
1.11.8 Asserting an Act Did Not Occur with a Reason
The negationInd attribute, if true, specifies that the act indicated was observed to not have occurred ...

Based on this I believe the discharge medication negationInd attribute should be associated with the act and not the related/contained substanceAdminstration.