In the database, deleted all the records in the topics table that had no instances pointing to them (either never had any or the topic had been collapsed into another topic, e.g. ChHx into Chinese History).
Checked all the ids for the about to be deleted topics to ensure no instances pointing to them in the articles table. Found only one instance of a pointer to id 148 (originally coded as "X" by author), which I deleted from the field in the articles record.
Updated topics.txt, and sent JL and email saying if he wanted to collapse any more topics, I'm pretty confident we could do it without problem, though we are no longer able to use the text files to rebuild the db content if necessary, as they contain pointers to non-existant topic id's, though a bunch of global search and replaces would solve that.