If you havent exited ioftpd then the dirs may still be in the cache.
A simlpe way to resolve the issue is to make a small sript that deletes the .ioFTPD file after an upload and then using ioRecache to mark the dir as dirty (un thus auto recreate the .ioFTPD file).
Now I havent tested it but ioRecache does resolve delete directories and files and symlinks by telling io to drop the cache of the dir.
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