You're talking about
files but you're checking the
dir log, there's a little problem there
No, ioBanana doesn't update the transfer.log (that's where filenames are stored) on DELE. You have to undupe those files.
On a side note, I don't recommend using the file dupechecker. Dupechecking dirs, adding XDUPE support and denying resume / overwrite is usually enough (and faster).