When you are uploading/downloading files you have 2 connections to the server. One control connection to send command and receive replies from the server and one data connection to send/receive files.
Sending NOOP during transfers (which is another option than sending NOOP when you are idling) helps to keep the control connection open. Indeed, the control connection can timeout during the file transfer and thus FlashFXP can't send the command to send/retrieve the next file and is forced to reconnect.
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