So for me you would either have to set all the options before the -SS command:
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-C_EXPORT_FMT PLY -PLY_EXPORT_FMT ASCII -AUTO_SAVE ON -NO_TIMESTAMP
Or use -AUTO_SAVE OFF before anything so as to be sure that the intermediate commands don't produce files each time, so as to only save them at the end of the process. As by default all commands like -SS will automatically save the result.
If you keep the AUTO_SAVE feature, then you can remove the call to -SAVE_CLOUDS.
And -CLEAR is not necessary if it's at the end of the command line, as it's automatically done by CC on completion.
But... this does not explain why you don't see any file created. As even with the above command line, you should have 2 sets of files! When you don't use -SILENT, do you see a message that states that a file has been saved? With a path? If yes, and if no file has been created, maybe it's due to some limited access rights?