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That meant my ClearLinkBetween method could no longer assume the mere presence of a linking record. I changed the code to this:

CML_Data_ManyToManyLinks.ClearLinkBetween         procedure(long leftRecordID,long rightRecordID)
    code
    if self.GetLinkRecord(leftRecordID,rightRecordID)
        self.LinksDataQ.IsLinked = FALSE
        put(self.LinksDataQ)
    end

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There's still work to be done here, not least of which is adding some measure of error handling. But this code does work. The unit tests pass, and in my UITest program my checkbox settings are preserved between runs.