I’ve been keeping a close eye on the Maildirs in question and they haven’t seemed to fill up with any duplicate messages, or Spam that seems out-of-ordinary.
My running hypothesis right now is that she was hit with a large bolus of spam, which queued up before SA, and got jammed up there when sa-learn was trying to chew through the huge amount of files in her .Spam/cur. RAM exhaustion caused the server to kill processes, which confused server-processes and mail-client as to what had been processed, resulting in duplicated messages.
After I purged the .Spam/cur, the old messages sitting in some queue before SA needed a few days to process.
I also helped her manually unsubscribe from the hundreds of legitimate lists she had put herself on for various retailers.