technically you shouldn't recieve messages during a transfer, by design and following the FTP RFC, it should come after the transfer has completed.
Most ftp servers do not allow commands to be sent during a transfer, some windows ftp servers are an exception. Since there is no simple and 100% perfect way to indentify windows ftp servers that allow commands during a transfer, FlashFXP treats all ftp servers the same and simply doesn't allow any commands to be sent during a transfer.
You're best bet is to press the 'stop after current transfer' button and wait until the current file finishes and then send your reply.
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