I was going to ask why
mysqldump was trying to write dropped tables but I found that answer from this question, How do you remove reported non existing tables from mysql?.
.frm files from my datadir has resolved the
mysqldump issue of trying to dump non-existent tables. Now my question is how do I drop a table and have all references to it removed? I would have thought issuing the
drop table would remove all associated files in the directory. I am using
MyISAM so perhaps the issue is related to that.