Proper Way to Remove Mysql Tables 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?.

Removing the .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.
Just remove all three of the correlated table data files from the file system and that should ensure all traces are removed as per my understanding of 15.2 The MyISAM Storage Engine 

Each MyISAM table is stored on disk in three files:


.frm
.MYD
.MYI



  Each MyISAM table is stored on disk in three files. The files have
  names that begin with the table name and have an extension to indicate
  the file type. An .frm file stores the table format. The data file has
  an .MYD (MYData) extension. The index file has an .MYI (MYIndex)
  extension.
  
  Source




Further Resources


1.6.3 How to Repair MyISAM Tables