I think Neoxed posted a script to deal with those.
See ioftpd.com/scripts
Also, deleting all .ioFTPD files from any number of subdirectories is a one line DOS command :
del /a/s C:\Somedir\.ioFTPD
This will delete all .ioFTPD files from C:\Somedir and all subdirectories.
You can even replace 'del' by 'dir' beforehand to make sure what files it will delete.
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